Weekend batch
Avijeet is a Senior Research Analyst at Simplilearn. Passionate about Data Analytics, Machine Learning, and Deep Learning, Avijeet is also interested in politics, cricket, and football.
Free eBook: Top Programming Languages For A Data Scientist
Normality Test in Minitab: Minitab with Statistics
Machine Learning Career Guide: A Playbook to Becoming a Machine Learning Engineer
The bottom line.
Hypothesis testing, sometimes called significance testing, is an act in statistics whereby an analyst tests an assumption regarding a population parameter. The methodology employed by the analyst depends on the nature of the data used and the reason for the analysis.
Hypothesis testing is used to assess the plausibility of a hypothesis by using sample data. Such data may come from a larger population or a data-generating process. The word "population" will be used for both of these cases in the following descriptions.
In hypothesis testing, an analyst tests a statistical sample, intending to provide evidence on the plausibility of the null hypothesis. Statistical analysts measure and examine a random sample of the population being analyzed. All analysts use a random population sample to test two different hypotheses: the null hypothesis and the alternative hypothesis.
The null hypothesis is usually a hypothesis of equality between population parameters; e.g., a null hypothesis may state that the population mean return is equal to zero. The alternative hypothesis is effectively the opposite of a null hypothesis. Thus, they are mutually exclusive , and only one can be true. However, one of the two hypotheses will always be true.
The null hypothesis is a statement about a population parameter, such as the population mean, that is assumed to be true.
If an individual wants to test that a penny has exactly a 50% chance of landing on heads, the null hypothesis would be that 50% is correct, and the alternative hypothesis would be that 50% is not correct. Mathematically, the null hypothesis is represented as Ho: P = 0.5. The alternative hypothesis is shown as "Ha" and is identical to the null hypothesis, except with the equal sign struck-through, meaning that it does not equal 50%.
A random sample of 100 coin flips is taken, and the null hypothesis is tested. If it is found that the 100 coin flips were distributed as 40 heads and 60 tails, the analyst would assume that a penny does not have a 50% chance of landing on heads and would reject the null hypothesis and accept the alternative hypothesis.
If there were 48 heads and 52 tails, then it is plausible that the coin could be fair and still produce such a result. In cases such as this where the null hypothesis is "accepted," the analyst states that the difference between the expected results (50 heads and 50 tails) and the observed results (48 heads and 52 tails) is "explainable by chance alone."
Some statisticians attribute the first hypothesis tests to satirical writer John Arbuthnot in 1710, who studied male and female births in England after observing that in nearly every year, male births exceeded female births by a slight proportion. Arbuthnot calculated that the probability of this happening by chance was small, and therefore it was due to “divine providence.”
Hypothesis testing helps assess the accuracy of new ideas or theories by testing them against data. This allows researchers to determine whether the evidence supports their hypothesis, helping to avoid false claims and conclusions. Hypothesis testing also provides a framework for decision-making based on data rather than personal opinions or biases. By relying on statistical analysis, hypothesis testing helps to reduce the effects of chance and confounding variables, providing a robust framework for making informed conclusions.
Hypothesis testing relies exclusively on data and doesn’t provide a comprehensive understanding of the subject being studied. Additionally, the accuracy of the results depends on the quality of the available data and the statistical methods used. Inaccurate data or inappropriate hypothesis formulation may lead to incorrect conclusions or failed tests. Hypothesis testing can also lead to errors, such as analysts either accepting or rejecting a null hypothesis when they shouldn’t have. These errors may result in false conclusions or missed opportunities to identify significant patterns or relationships in the data.
Hypothesis testing refers to a statistical process that helps researchers determine the reliability of a study. By using a well-formulated hypothesis and set of statistical tests, individuals or businesses can make inferences about the population that they are studying and draw conclusions based on the data presented. All hypothesis testing methods have the same four-step process, which includes stating the hypotheses, formulating an analysis plan, analyzing the sample data, and analyzing the result.
Sage. " Introduction to Hypothesis Testing ," Page 4.
Elder Research. " Who Invented the Null Hypothesis? "
Formplus. " Hypothesis Testing: Definition, Uses, Limitations and Examples ."
Home » What is a Hypothesis – Types, Examples and Writing Guide
Table of Contents
Definition:
Hypothesis is an educated guess or proposed explanation for a phenomenon, based on some initial observations or data. It is a tentative statement that can be tested and potentially proven or disproven through further investigation and experimentation.
Hypothesis is often used in scientific research to guide the design of experiments and the collection and analysis of data. It is an essential element of the scientific method, as it allows researchers to make predictions about the outcome of their experiments and to test those predictions to determine their accuracy.
Types of Hypothesis are as follows:
A research hypothesis is a statement that predicts a relationship between variables. It is usually formulated as a specific statement that can be tested through research, and it is often used in scientific research to guide the design of experiments.
The null hypothesis is a statement that assumes there is no significant difference or relationship between variables. It is often used as a starting point for testing the research hypothesis, and if the results of the study reject the null hypothesis, it suggests that there is a significant difference or relationship between variables.
An alternative hypothesis is a statement that assumes there is a significant difference or relationship between variables. It is often used as an alternative to the null hypothesis and is tested against the null hypothesis to determine which statement is more accurate.
A directional hypothesis is a statement that predicts the direction of the relationship between variables. For example, a researcher might predict that increasing the amount of exercise will result in a decrease in body weight.
A non-directional hypothesis is a statement that predicts the relationship between variables but does not specify the direction. For example, a researcher might predict that there is a relationship between the amount of exercise and body weight, but they do not specify whether increasing or decreasing exercise will affect body weight.
A statistical hypothesis is a statement that assumes a particular statistical model or distribution for the data. It is often used in statistical analysis to test the significance of a particular result.
A composite hypothesis is a statement that assumes more than one condition or outcome. It can be divided into several sub-hypotheses, each of which represents a different possible outcome.
An empirical hypothesis is a statement that is based on observed phenomena or data. It is often used in scientific research to develop theories or models that explain the observed phenomena.
A simple hypothesis is a statement that assumes only one outcome or condition. It is often used in scientific research to test a single variable or factor.
A complex hypothesis is a statement that assumes multiple outcomes or conditions. It is often used in scientific research to test the effects of multiple variables or factors on a particular outcome.
Hypotheses are used in various fields to guide research and make predictions about the outcomes of experiments or observations. Here are some examples of how hypotheses are applied in different fields:
Here are the steps to follow when writing a hypothesis:
The first step is to identify the research question that you want to answer through your study. This question should be clear, specific, and focused. It should be something that can be investigated empirically and that has some relevance or significance in the field.
Before writing your hypothesis, it’s essential to conduct a thorough literature review to understand what is already known about the topic. This will help you to identify the research gap and formulate a hypothesis that builds on existing knowledge.
The next step is to identify the variables involved in the research question. A variable is any characteristic or factor that can vary or change. There are two types of variables: independent and dependent. The independent variable is the one that is manipulated or changed by the researcher, while the dependent variable is the one that is measured or observed as a result of the independent variable.
Based on the research question and the variables involved, you can now formulate your hypothesis. A hypothesis should be a clear and concise statement that predicts the relationship between the variables. It should be testable through empirical research and based on existing theory or evidence.
The null hypothesis is the opposite of the alternative hypothesis, which is the hypothesis that you are testing. The null hypothesis states that there is no significant difference or relationship between the variables. It is important to write the null hypothesis because it allows you to compare your results with what would be expected by chance.
After formulating the hypothesis, it’s important to refine it and make it more precise. This may involve clarifying the variables, specifying the direction of the relationship, or making the hypothesis more testable.
Here are a few examples of hypotheses in different fields:
The purpose of a hypothesis is to provide a testable explanation for an observed phenomenon or a prediction of a future outcome based on existing knowledge or theories. A hypothesis is an essential part of the scientific method and helps to guide the research process by providing a clear focus for investigation. It enables scientists to design experiments or studies to gather evidence and data that can support or refute the proposed explanation or prediction.
The formulation of a hypothesis is based on existing knowledge, observations, and theories, and it should be specific, testable, and falsifiable. A specific hypothesis helps to define the research question, which is important in the research process as it guides the selection of an appropriate research design and methodology. Testability of the hypothesis means that it can be proven or disproven through empirical data collection and analysis. Falsifiability means that the hypothesis should be formulated in such a way that it can be proven wrong if it is incorrect.
In addition to guiding the research process, the testing of hypotheses can lead to new discoveries and advancements in scientific knowledge. When a hypothesis is supported by the data, it can be used to develop new theories or models to explain the observed phenomenon. When a hypothesis is not supported by the data, it can help to refine existing theories or prompt the development of new hypotheses to explain the phenomenon.
Here are some common situations in which hypotheses are used:
Here are some common characteristics of a hypothesis:
Hypotheses have several advantages in scientific research and experimentation:
Some Limitations of the Hypothesis are as follows:
Researcher, Academic Writer, Web developer
As you were browsing something about your browser made us think you were a bot. There are a few reasons this might happen:
To regain access, please make sure that cookies and JavaScript are enabled before reloading the page.
It was good you gotta believe me.
The following fact is indisputable: Steak tastes its best when it’s medium rare. The same is true for salmon, tuna, and really, any other cut of quality seafood, which is often served either entirely raw or lightly seared. We have evolved past the outmoded kitchen guidelines that claimed that pork must be cooked to a parched, bone-white opacity, starving the meat of its luxuriant juices. And then there’s duck, which, despite being poultry, tastes most heavenly when it’s crisp on the outside and cherry red in the middle.
When you bundle all of these observations together, you are left with no choice but to conclude that animal protein is most delicious when slightly undone. If you extrapolate this point even further, then surely, undercooked chicken must also be outrageously yummy, and we’ve all been missing out on the epicurean range of America’s favorite dinner plate for generations. It’s a hypothesis worth considering because, if you haven’t noticed, chicken sucks. It’s boring. The amount of attention necessary to inject the faintest whiff of dynamism into the bird has been the bane of chefs for centuries. And if strategic undercooking is the secret to unlocking the protein’s finer qualities, then it must be a noble pursuit. This is the basis of my lifelong fascination with the culinary potential of pink chicken, and why I set out to find a way to sink my teeth into a wad of breast meat cooked to an exquisite medium rare.
I have always been an adventurous eater. I’ve sampled ruby-red horse sashimi in Tokyo, poached duck’s blood in Chongqing, and steamed mantis shrimp—with all of its spindling centipedelike legs intact—in Bangkok. As such, I tend to think Americans are annoying and precious with what they allow into their stomachs. Thankfully, the culture appears to be in the midst of a nutritional reckoning, with countless influencers pushing heterodox eating habits on their platforms. Raw milk is having a moment , so is raw honey , and raw liver . We must also mention the existence of the Instagram account Raw Chicken Experiment , which has garnered over 400,000 Instagram followers, all of whom watch an unnamed man consume raw chicken, day after day, until he gets a “tummy ache.” (Currently, he’s on his 101 st dinner of refrigerator-cold unpasteurized poultry.)
However, it must be reiterated that no food scientist on the planet would endorse the idea of consuming chicken that hasn’t been fully pasteurized. “We risk consuming bacteria which can lead to food poisoning,” said Julia Zumpano, a dietician at the Cleveland Clinic who laid out the assortment of bowel-destroying microbes present in raw chicken, E. coli being the most common. Zumpano, like every other registered dietician, recommends bringing poultry of any variety up to 165 degrees , which is a temperature hot enough to incinerate all of those bacterial agents, guaranteeing a safe digestion. This isn’t a regulatory overreach, either. According to the Centers for Disease Control and Prevention , 1 out of every 25 packages of chicken in the grocery store is contaminated with salmonella, which means that if you are routinely chowing on the rubbery pink of unpasteurized poultry, there is a good chance that you may soon be making several grim treks to the bathroom. Humans have understood this concept for millennia. In American colonial homes, one of the most popular ways to cook chicken was to hang it from a string in front of a fireplace. According to the Greenwich Historical Society, children would often be tasked with spinning the string in front of the hearth, to ensure every part of the bird was fully pasteurized before eating.
But that hasn’t stopped some of the planet’s more intrepid eaters from throwing caution to the wind, and scarfing down raw chicken. After all, if you know where to look, you can find chefs willing to experiment with the dark arts of undercooked poultry. The most famous of these traditions is surely Japan’s notorious torisashi , colloquially known in the Western Hemisphere as chicken sashimi, which is essentially chicken breast that’s either served completely raw or has been put under intense heat for a couple of milliseconds until its left with a charred exterior surrounding a wet, cold, coral-pink interior. Torisashi is hard to find in America, though you can track it down at certain audacious yakitori counters—like the famous Berkeley restaurant Ippuku, which contains a whole gallery on its Yelp page of patrons gawking at its chicken tartare . (“I’ll still give this place three stars even though I got food poisoning,” reads one review. “Other than that it’s a pretty legit joint.”)
Torisashi tends to be more of a regional delicacy in Japan, particularly in the Kyushu city of Miyazaki. The dish has an ardent cult of fans, like 39-year-old New Zealander William Heath, who tells me he was previously married to a woman from Miyazaki. During his trips to the island, Heath estimates he ate torisashi over 200 times, and he rates it as one of his favorite meals.
“It has the texture of sashimi salmon. A meaty yet yielding texture. Most times I’ve eaten it, it’s been with a sear, like a blue steak. Generally with a ponzu sauce, white onions, and wasabi. It’s not slimy like what you’d expect with raw chicken,” he said. “Some places serve it with a raw egg. Imagine that in the Western world! If you can push yourself a little bit beyond what you’ve been taught your whole life, you open up to a whole world of tastes and flavors that are, without being dramatic, awe-inspiring.”
Heath said he was never concerned about the potential health fallout from the dish—particularly when he was eating with other diners who reveled in the sinewy tang of raw breast meat. (“Japanese food is notorious for being stringent to cleanliness,” he said. “And any fast food seen as safe, like McDonald’s or Subway, has the chance to make you ill.”) Of course, Japan’s own Ministry of Health has pushed back on Heath’s assertion that the country has mastered the art of preparing unpasteurized poultry without the risk of personal contamination, to the point of issuing a warning to travelers imploring them to avoid consuming “raw or inadequately cooked chicken” while visiting the island. I’m also not surprised to hear that despite Heath’s fondness for the dish, he’s never attempted to replicate torisashi himself.
“I don’t have the skills, knowledge, or expertise to do it correctly,” he said, comparing torisashi, aptly, to the highly toxic fugu pufferfish that appears on the menu of certain high-end sushi restaurants.
All of this is to say if I wanted to eat undercooked chicken without maxing out my deductible, then torisashi was probably off the table. I needed to think outside the box, which, before long, brought me to the wondrous world of sous vide . The French innovation, in which protein is placed into vacuum-sealed plastic bags and poached in water that has been heated to an uber-precise temperature, is most commonly used to cook red meat. But I had heard that there existed a method to use the machine to bring chicken up to a delectable 140 degrees—the same temperature range for a ruddy medium steak—while still eradicating those pesky colonies of E. coli and salmonella.
The method was popularized by J. Kenji Lopez-Alt, a chef and food writer, and the author of The Food Lab: Better Home Cooking Through Science . In an article he published on Serious Eats , Lopez-Alt argued that pasteurizing chicken is a process that involves both time and heat. Yes, the prescribed 165-degree threshold for poultry will eliminate hostile bacteria in the blink of an eye, but holding the protein at a lower temperature will eventually accomplish the same task over a longer cooking duration. That might be difficult to accomplish on a finicky stovetop, but a sous vide circulator, built to maintain a specific level of heat for hours on end, is perfect for the job.
“At 165 degrees you achieve pasteurization nearly instantly. It’s the bacterial equivalent of shoving a stick of dynamite into an anthill,” wrote Lopez-Alt. “At 136 degrees, on the other hand, it takes a little over an hour for the bacteria to slowly wither to death in the heat.”
Many in the sous vide community have become enthralled by the promise of 140-degree chicken. Cole Wagoner, who works in marketing and frequently shows off the dish on his social feeds , claims that subtemperature poultry is so radically different from the staid blandness of conventional roasted chicken breast that it can almost have a psychotropic effect on a diner’s brain.
“It’s the difference between a medium-rare steak and a well-done steak,” he said. “You cut into it and see an immediate difference. It’s the same flavor, but the amount of natural moisture you get with the sous vide method is profound.”
But Wagoner also mentions that his dish tends to get a polarized response from his dinner guests. Sometimes, after he carves a light-pink chicken breast at the table, his friends and family will whip out their phones and order a circulator for themselves to get in on the revolution. Other folks—like Wagoner’s parents—are so disgusted by the sight that they refuse to even try it.
“I haven’t had many converts,” continued Wagoner. “I haven’t had people say, ‘That looks gross’ and after trying it, they decide they love it.”
After trying the method myself, I can understand where Wagoner is coming from. I arrived at the Slate office kitchen armed with two boneless, skinless chicken breasts, which were subsequently bagged, vacuum-sealed, and dunked in a colleague’s circulator. We set the timer for two hours, at 140 degrees, in accordance with the recipe outlined by Lopez-Alt. I didn’t have high hopes. Poached chicken, in any variety, is never the most visually appealing dish, and once the timer went off, we pulled two grotty, lukewarm hunks of poultry from the depths of the machine. Both of them had turned pallid in their bags, which were stained by the muddy secretion of their juices. Bon appétit ?
To my relief, nothing about the chicken breasts appeared to be viscerally undercooked. Yes, they lacked some of the appetizing wrinkles chefs use to spruce up some of the more tiresome items in their inventory—no grill marks, or cast-iron caramelization, or evidence of a marinade or spice blend—but they didn’t look poisonous, either. My colleague had brought along a kitchen torch, and he sizzled the exterior until the chicken looked less pale and more edible. We got to carving afterward, and the knife passed through the meat with almost no resistance, revealing a few light-pink rings complementing the ruffled whiteness of the protein. My dream had finally come true. Medium-rare chicken was at hand.
Wagoner was right. So was Heath. Undercooked chicken will change everything you believed about cooking poultry. The chicken was unbelievably soft. Almost gelatinous, with the physical consistency of an overnight brisket. It was juicy to the point of being disorienting. Slicing into the breast meat was like puncturing a water balloon—ultra-indulgent and almost sinful, you could peel off splinters of white meat with your fingertips and let them melt in your mouth. The flavor profile didn’t change much, though. This was still definitely chicken, but a heightened, more primal chicken—almost gamey, bearing evidence of once being alive.
But was it good? That’s a question I’ve been struggling to answer. Like most Americans, I have been conditioned to expect a very narrow set of possibilities with my chicken. It is the weeknight protein, a dish that is primarily kept on the menu to cater to fussy eaters, and even at its best—say, a whole roast bird on a perch of root vegetables, golden brown and oozing with rendered butter—the dining experience is pleasantly mild. But at 140 degrees, chicken subverts so many of those comforts that it no longer fits into its domestic reliability. I imagine sitting at a dinner table with my family who are all wide-eyed and zonked-out after experiencing this decadent chicken odyssey—a version of their favorite boring white meat with all of its positive qualities cranked up toward an overripe extreme. We’d be satiated but overwhelmed, and I think that makes sous vide chicken difficult to dish up on a random Tuesday evening.
That said, I was pleased to confirm my theory. Yes, as it turns out, a medium-rare chicken does taste amazing, in perfect lockstep with all the other animals I like to eat. I wrapped up the other breast and packed it away, and started fantasizing about all the ways it could be served. Maybe a medium-rare chicken salad? Or a medium-rare chicken cutlet, ripped out of the sous vide and then breaded and flash-fried? The possibilities were endless. First things first though, I offered a forkful of my experiment to some of my other Slate colleagues, hoping that they, too, would see the light. I was rejected across the board. No surprises there. We may have finally come up with a way to make medium-rare chicken, but it might be much longer before anyone wants to eat it.
Loading metrics
Open Access
Peer-reviewed
Research Article
Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing – original draft, Writing – review & editing
Affiliations Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America, UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California, Irvine, Irvine, California, United States of America
Roles Conceptualization, Methodology, Supervision, Validation, Writing – review & editing
Affiliation Department of Physics and Center for Soft Matter Research, New York University, New York, New York, United States of America
Roles Conceptualization, Formal analysis, Funding acquisition, Methodology, Project administration, Resources, Supervision, Validation, Writing – review & editing
* E-mail: [email protected]
Affiliations Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America, UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California, Irvine, Irvine, California, United States of America, Department of Chemical & Biomolecular Engineering, University of California, Irvine, Irvine, California, United States of America, The NSF-Simons Center for Multiscale Cell Fate Research and Sue and Bill Gross Stem Cell Research Center and Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
Understanding muscle contraction mechanisms is a standing challenge, and one of the approaches has been to create models of the sarcomere–the basic contractile unit of striated muscle. While these models have been successful in elucidating many aspects of muscle contraction, they fall short in explaining the energetics of functional phenomena, such as rigor, and in particular, their dependence on the concentrations of the biomolecules involved in the cross-bridge cycle. Our hypothesis posits that the stochastic time delay between ATP adsorption and ADP/Pi release in the cross-bridge cycle necessitates a modeling approach where the rates of these two reaction steps are controlled by two independent parts of the total free energy change of the hydrolysis reaction. To test this hypothesis, we built a two-filament, stochastic-mechanical half-sarcomere model that separates the energetic roles of ATP and ADP/Pi in the cross-bridge cycle’s free energy landscape. Our results clearly demonstrate that there is a nontrivial dependence of the cross-bridge cycle’s kinetics on the independent concentrations of ATP, ADP, and Pi. The simplicity of the proposed model allows for analytical solutions of the more basic systems, which provide novel insight into the dominant mechanisms driving some of the experimentally observed contractile phenomena.
Explaining the intricate workings behind muscle contraction remains a fundamental challenge in our field. In this work, we develop a computational model of the sarcomere designed to unravel the basic energetics of sarcomere contraction, and we place major emphasis on the stochastic nature of the reactions in the cross-bridge cycle. The main goal was to illustrate how dynamic processes such as rigor are contingent upon the concentrations of biomolecules governing the kinetics of the cross-bridge cycle. We posited that including the free energy contributions associated with ATP and ADP/Pi as separate reaction steps could unveil previously inaccessible aspects of sarcomere contraction. To test this hypothesis, we constructed a stochastic-mechanical half-sarcomere model whose kinetics explicitly account for the fact that ATP and ADP/Pi interact with myosin at different times in the cross-bridge cycle. Our findings demonstrate a dependence of sarcomere outputs on independent concentrations of ATP, ADP, and Pi, a phenomenon exclusively reproducible with our hypothesized free energy framework. Lastly, the conceptual simplicity of our model enables analytical solutions for elementary systems, affording new insights into the principal drivers governing experimentally observed contractile phenomena.
Citation: Schmidt AA, Grosberg AY, Grosberg A (2024) A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function. PLoS Comput Biol 20(8): e1012321. https://doi.org/10.1371/journal.pcbi.1012321
Editor: Daniel A. Beard, University of Michigan, UNITED STATES OF AMERICA
Received: February 26, 2024; Accepted: July 12, 2024; Published: August 5, 2024
Copyright: © 2024 Schmidt et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: The code for this manuscript is available on github: https://github.com/Cardiovascular-Modeling-Laboratory/SarcomereModel .
Funding: This work was partially supported by NIH T32HL116270 (AS), DoD NDSEG Fellowship (AS), NSF CMMI-2035264 (AG), NSF CMMI-2230503 (AG), NIH R03 EB028605 (AG). The funders did not play a role in the study design, data collection and analysis, decision to publish, nor preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Force generation in striated muscle is regulated by the complex interactions between the actomyosin complex and ATP, ADP, and inorganic phosphate (Pi). Changes in these concentrations can significantly affect muscle contraction, relaxation, and the overall energy balance of contractile cells. Both decreased ATP levels and elevated ADP and Pi levels have been observed in several pathological conditions including heart failure, ischemia, and mitochondrial disorders [ 1 – 5 ]. Despite the importance of investigating the effects of varying ATP, ADP, and Pi concentrations on muscle, the mechanisms that drive the dynamical contractile response are not fully understood.
The generation and maintenance of contractile mechanical stress in striated muscle is performed by sarcomeres black, the basic contractile units of striated muscle. Sarcomeres consist of a three-dimensional lattice of two main types of filaments–thick filaments, which are bound to the center of the sarcomere at the M-line and the ends of the sarcomere at the Z-lines (via titin), and thin filaments, which are bound only at the Z-lines [ 6 , 7 ]. During concentric contraction, the sarcomere shortens as thick filament myosin heads pull thin filaments toward the center of the sarcomere. This pulling force is generated via the cross-bridge cycle, which involves interactions between a single myosin head and a discrete binding site on the actin filament [ 7 , 8 ]. In each cycle, myosin ATPase hydrolyzes one ATP molecule, whose free energy of hydrolysis is partially converted into mechanical work during the power stroke [ 8 , 9 ]. Consequently, ATP availability and the ease of release of its hydrolysis products, ADP and Pi, play integral roles in the possible force generated by the muscle. Therefore, recreating these dynamics of the cross-bridge cycle could be essential for sarcomere models.
For over half a century, a variety of models have been developed to recapitulate the behavior of a sarcomere [ 10 – 27 ]. A review of these models can be found within Niederer et al.’s work [ 28 ] and within the Introduction of Mijailovich et al.’s 2016 MUSICO paper [ 21 ]. Many of the stochastic, spatially explicit models recreate the discrete locations and interactions of the sarcomeric filaments in space (1 to 3 dimensions), allow them to capture the nuances of force generation at a granular level, the propagation of mechanical signals, the heterogeneity in cross-bridge binding and sarcomere lengths, and the internal tension contributions by other compliant components of the sarcomere. However, the kinetic schema of some of these existing models needs to be augmented with rate constants that properly include the free energy contributions of the concentrations of ATP, ADP, and Pi in order to cover a wider variety of experimental conditions [ 14 – 23 ]. A physiologically relevant partitioning of these chemical potentials would also allow for closer examination of the effects of ATP availability, as well as ADP and Pi excess, on sarcomere force generation and maintenance. Conversely, while some probabilistic sarcomere models include the impact of all three molecules in their cross-bridge rate kinetics [ 25 – 27 ], they do not possess the same advantages as stochastic and discrete lattice sarcomere models [ 29 , 30 ].
In this work, we detail the formulation of a spatially explicit, two-filament half-sarcomere model capable of elucidating force generation profiles at varying levels of ATP, ADP, and Pi. Specifically, we employed this model to predict the sarcomeric ATP consumption associated with different levels of contractile force. Thus, we created a novel stochastic-mechanical sarcomere model that tracks discrete node locations and implements a direct dependence of cross-bridge rate kinetics on the concentrations of ATP and its hydrolysis products. The findings of this work yield new insight on the energetics of force generation in muscle tissues.
We adopt, with small modifications, the two-filament sarcomere model analyzed in previous studies [ 10 , 14 , 16 ]. Our model is a composition of three aspects, the first of which is the half-sarcomere’s geometry. This aspect simplifies the three-dimensional interactions between thick and thin filaments to a one-dimensional system. The second aspect, the mechanics of the half-sarcomere, assumes the sarcomere behaves as a set of linearly elastic (Hookean) springs, and is described by a set of linear equations that combine the geometric constants of the sarcomere with the spring constants of the sarcomere’s physiological components. The final aspect of this model, which underpins the innovation introduced in this paper, is the chemical kinetics, which describe the stochastic chemical transformations through the cross-bridge cycle. Following the majority of previous works, we assume that the elastic equilibrium in the system is achieved comparatively very fast, such that chemical transformations occur essentially between various elastically equilibrated states. To describe the chemical cycle, we adopt the middle ground between the simplest two-state models [ 10 ] and 9 state models [ 30 ], and employ the three-state description, which is widely considered the minimal number of states appropriate for recapitulating a cross-bridge’s biomechanics [ 10 , 14 , 16 , 21 ].
The geometry of the half-sarcomere includes two filaments that are each composed of an array of nodes ( Fig 1 ). Each node on a thin filament ( a n ) represents a discrete actin binding site to which a myosin cross-bridge can bind. Thick filament nodes ( m n ) represent the base of each myosin cross-bridge. In addition to the total number of actin nodes, N a , and the total number myosin nodes, N m , there is a node at the end of each filament: one at the Z-line ( a Z ) and the M-line ( m M ) for the thin and thick filaments respectively. This results in N a + N m + 2 total nodes. Titin was incorporated into this model as a spring element binding the Z-line to the myosin node most distal to the M-line ( Fig 1A , green spring). While Fig 1 is depicted in two dimensions, it is only done so for the clarity of presentation. The forces and displacements in the model are assumed to exist solely along the x-axis parallel to the thick and thin filaments. Elements of physiological spacing were incorporated into this study’s model in order to preserve, at least in part, the properties of the higher order three-dimensional nature of physiological sarcomeres (details in Section A of S1 Text ). While this one-dimensional, two-filament system does not fully capture the three-dimensional helical geometry of a sarcomere in vivo , the simplicity of the system makes it a valuable tool for interrogating the mechanical and chemical dynamics of force generation relevant to this paper.
(A) Half-sarcomere model showing the geometry of a system containing two actin nodes and two myosin nodes. Cross-bridges are bound, connecting the thick and thin filaments. (B) Schematic showing the three potential mechanical states of a cross-bridge. State 1 shows a cross-bridge unbound from the thin filament. State 2 shows a bound, pre-power stroke cross-bridge in a low force bearing state. State 3 shows a bound, post-power stroke cross-bridge in a high force bearing state. In state 3, the cross-bridge has also undergone a conformational change where the cross-bridge rest length ( b 0 ) has shortened by the length of a power stroke ( d ps ). The model is one dimensional, but this figure illustrates the model in two dimensions for clarity. All forces in this model are assumed to be one-dimensional, parallel to the filaments.
https://doi.org/10.1371/journal.pcbi.1012321.g001
As cross-bridge binding and/or force generation within the half-sarcomere causes distortions in the spring elements of the model, both K and V vary their components accordingly. At any moment, the mechanical equilibrium of the model, and more specifically the location of each node within the lattice, was calculated from Eq 1 using MATLAB’s internal system of linear equations solver (details in Appendix B).
Shorthand for the biochemical states of the actomyosin complex are displayed in black frames: A-actin, M-myosin, ATP-adenosine triphophate, ADP-adenosine diphosphate, Pi-inorganic phosphate. All elements in each black box are bound. Between state 3 and state 1, ATP binds the actomyosin complex and is hydrolyzed. Rates for the transitions between each state are labeled such that k ij represents the transition rate from state i to j . Association of ATP to the actomyosin complex and the dissociation of ADP and Pi from the actomyosin complex are indicated at the appropriate transition.
https://doi.org/10.1371/journal.pcbi.1012321.g002
Shorthand of the biochemical states of the actomyosin complex are framed in black (key in Fig 2 caption). Transition states are denoted by dashed lines and dashed frames. Δ G hyd = Δ G T assoc. + Δ G T hydr. + Δ G D,Pi rel. . Free energy of association of ATP is Δ G T assoc . . Free energy of ATP hydrolysis is Δ G T hydr. . Free energy of of ADP and Pi release from actomyosin is Δ G D,Pi rel. . G ADP,Pi = k B T ln([ADP][Pi]). G ATP = k B T ln([ATP]). Note: The free energies of each state depicted in this free energy landscape assume there is no cross-bridge deformation, and therefore do not include the elastic potential energy contributions of such deformations. The complete free energies of each state, including elastic potential energies, are fully defined in Eqs 2 – 5 .
https://doi.org/10.1371/journal.pcbi.1012321.g003
A reference energy of 0 was set for the free energy of the state 1 ( Eq 2 ). Traveling through each cycle requires the addition of an ATP from the environment, thus we defined state 1’ as the energy baseline of the following new cross-bridge cycle ( Eq 5 ). All parameters were taken from literature (details in Section D of S1 Text ), and then fine-tuned to match the physiological duty ratio [ 31 ]. Fine tuning of parameters may need to be adjusted within their pre-determined ranges depending on the specific geometry of the system. For a one-myosin system, all variables and parameters are defined in Table 1 . The rate constants along with their equilibrium ratios were defined as follows, using the notations from Table 1 :
Variables and the corresponding units or values used in the sarcomere model. Values were selected after a parameter exploration was performed on a range of values pulled from literature from both models and experiments (details in Section D of S1 Text ).
https://doi.org/10.1371/journal.pcbi.1012321.t001
The solution implementation in MATLAB is discussed in detail in Sections B and C of S1 Text . For all simulations in this investigation, the sarcomere was allowed to spontaneously contract (i.e. no assigned velocity of shortening), with full calcium activation of all binding sites (actin nodes) along the thin filament.
The model implementation was verified against the inherent physics of the system. For example, we compared the energy input into the system via ATP hydrolysis to the total elastic potential energy of the springs in the system. Model outputs were compared to those reported in experimental literature, such as ranges of values for ATP consumption, peak force of a single myosin, and force per myosin in larger systems. Independently, reports of rigor concentrations of ATP were compared to predictions made by this model.
Before investigating the impact of the new free energy schema on sarcomere behavior across a range of [ATP] and [ADP][Pi] concentrations, we first validated the model by simulating a single myosin system at the standard normal concentrations for ATP, ADP, and Pi: 5 mM, 0.03 mM, and 3 mM respectively [ 13 , 29 , 52 , 53 ]. This simulation revealed a peak force of 3 pN per myosin. This value is consistent with a previous literature range of ∼1–7 pN [ 32 , 54 – 57 ]. Next, a half-sarcomere consisting of 16 myosin and 24 actin nodes was simulated ( Fig 4A ) with the same parameters as a single myosin system ( Table 1 ). The average sarcomeric force output was 2.1 pN (dashed line Fig 4A ), resulting in a time-averaged force per myosin of 0.13 pN. The estimation method described previously for organ-scale contraction [ 58 ] was applied to data from other experiments, including muscular thin films (tissue-scale) and traction force microscopy (cell-scale) [ 59 – 63 ], which resulted in the range of forces per myosin in different systems to be 0.04–1 pN. Thus, we conclude that our values of time-averaged force/myosin are within physiologically expected ranges.
Single half-sarcomere consisting of 16 myosin and 24 actin nodes under (A-B) normal ([ATP] = 5 mM) and (C-D) reduced ([ATP] = 0.5μM) ATP conditions. (A,C) Force output profile denoted by black circles. Average force denoted by the dashed line. Force averaged over a sliding window of (A) 12 ms and (C) 14 ms denoted by blue lines with blue diamonds. (B,D) ATP consumption rate (molecules/s) denoted by black circles. ATP consumption rate averaged over a sliding window of 50 ms denoted by green diamonds.
https://doi.org/10.1371/journal.pcbi.1012321.g004
To validate the order of magnitude of ATPase activity, ATP consumption rate per myosin was calculated by approximating the density of myosin heads per muscle tissue volume (0.48–1.2 × 10 17 myosin/cm 3 ) from literature estimates of myosin concentration in muscle [ 64 – 67 ]. Based on experimental data from isometrically and concentrically contracting muscle, an ATP consumption estimate would be on the order of 1–120ATP/s per myosin [ 41 , 65 – 76 ]. If one takes into account the proportion of myosin hypothesized to actually be participating in contraction [ 77 ], an estimate would yield a range of 2–240ATP/s per myosin (further details in Section E of S1 Text ). In the model, ATPase activity was then quantified by tracking the number of myosin transitions (per unit time) from state 3 to state 1–the transition that involves the hydrolysis of one ATP molecule ( Fig 4B ). To avoid biases from the initialization of the contraction simulation, plateau ATP consumption rates were calculated as the mean rate after the rate first exceeds 98% of the maximum consumption rate. The plateau ATP consumption rate of the single 16-myosin sarcomere system was 1400ATP/s ( Fig 4B ) or about 88ATP/s per myosin, matching our physiological estimates.
Having validated the model, we next demonstrated that there was a significant change to the behavior of the sarcomere when the concentration of [ATP] was changed to 0.5 μM ( Fig 4C and 4D ), while concentrations of [ADP] and [Pi] were maintained at those found under standard conditions. As can be seen from the force plot ( Fig 4C ), the sarcomere exhibited rigor like behavior with slow “ratcheting”–characterized by repeated cycles of brief contractile force increases followed by periods of force stagnancy due to lack of ATP. The effect of reduced [ATP] also manifests itself in the ATP consumption rate ( Fig 4D ), which is significantly reduced compared to that of the system under standard conditions.
To further explore this, we considered situations with varying values of concentrations of [ATP] and [ADP][Pi]. If all transition rates were to be assumed dependent only upon the ratio [ATP]/[ADP][Pi], all fluctuations in the sarcomere, as well as the average times a myosin head spends in states 1, 2, and 3, would also solely depend on only the ratio [ATP]/[ADP][Pi]. Fig 5A demonstrates how very different values of [ATP] and [ADP][Pi] can have ratios that are the same (equivalent ratios displayed in the same color), resulting in the diagonal symmetry. This point is illustrated in Fig 5B , where we show what the ATP consumption for a single myosin system would look like if state transitions were dependent upon only the ratio [ATP]/[ADP][Pi]. Such a system would have state transition rates that are equivalent as long as the ratio [ATP]/[ADP][Pi] is the same.
Comparison of free energy schema in terms of ATP consumption (A) Ratios of [ATP] to [ADP][Pi]. (B) Plateau ATP consumption rate for a one-myosin system where attachment of ATP and detachment of ADP and Pi effectively happen simultaneously, allowing for no time delay between these events. For such a model, the rate kinetics, and thus ATP consumption, depend only the ratio of [ATP]/[ADP][Pi]. (C) Our model’s plateau ATP consumption rate simulation results for a one-myosin system. Note the plot’s asymmetry compared to (B) and the proximity of the standard physiological conditions (bold red lines) to the crossover between regimes. One-myosin simulation results of (D) Duty ratio and (E) Average force for various ([ATP], [ADP][Pi]) combinations. (F) Changes in duty ratio (black), average force output (purple), and plateau ATP consumption rate (blue) at standard physiological [ADP][Pi] and varying [ATP] concentrations. (B-F) Standard physiological conditions are denoted by bold red lines ([ATP] = 5 mM, [ADP][Pi] = 0.09 mM 2 ). Dashed white/gray lines denote the the [ATP] concentration associated with the onset of rigor ([ATP] = 0.5 mM) [ 75 , 79 ]. (C-F) n = 10.
https://doi.org/10.1371/journal.pcbi.1012321.g005
The ability of our model to consider separately how [ATP], [ADP], and [Pi] affect the transition rates allowed us to interrogate imbalances in these molecules (Eqs 2 – 14 ). Our model demonstrated that, for a single myosin simulation across varying ([ATP], [ADP][Pi]) combinations, there is in fact an asymmetry in ATP consumption that directly results from the appropriate allocation of the overall free energy change of the cross-bridge cycle ( Fig 5C ). Importantly, the physiological concentration of [ATP] falls within the range of the observed transition region roughly from 10mM to 5 μM (yellow to blue, Fig 5C ). This change in regime is also visible in one myosin system simulation outputs for duty ratio (the fraction of time a myosin head spends in state 3 [ 31 , 48 , 78 ]) and average force ( Fig 5D–5F ).
Furthermore, the ATP concentration at which the system begins to exhibit rigor-like characteristics (dashed white/gray line, Fig 5C–5F ), indicated by a rise in duty ratio, is consistent with the one experimentally observed with the onset of rigor ([ATP] ≤ 0.5 mM) [ 75 , 79 ]. Notably, the free energy schema utilized by this model was constructed completely independent of any experimental results on rigor-inducing concentrations of [ATP]. Therefore, the alignment between our model’s predictions and experimental values acts as an independent validation of the proposed free energy schema.
Next, we examined duty ratio, average force, and plateau ATP consumption rate for a simulation of a 16-myosin half-sarcomere model with the same parameters as a single myosin system ( Table 1 ) across varying ([ATP], [ADP][Pi]) combinations and qualitatively observed similar asymmetry in duty ratio, average force, and plateau ATP consumption rates ( Fig 6A–6C ). For example, in the region with lower than normal [ATP], and low to normal [ADP][Pi], multi-myosin half-sarcomere systems will ratchet up the thin filament to a greater degree of shortening (Figs 4C and 6A–6C ). This ratcheting behavior is what is expected for muscle that can contract but not relax. While in other regions, such as physiological-adjacent conditions, the system’s force output fluctuates more naturally (Figs 4A and 6A–6C ). In examining the regime change associated with the onset of rigor at normal [ADP][Pi] (0.09 mM 2 ), we noted a shift from where the transition is reported physiologically by one order of magnitude ( Fig 6D–6E ). We hypothesized that this is likely caused by the more complex internal tensions of a multi-myosin system shifting the duty ratio to lower than normal ( Fig 6A and 6D ). The first step in testing this hypothesis was to evaluate whether internal tensions can change expected sarcomere deformations. Indeed, the effective sliding distance (ESD) of the one-myosin system simulation is actually less than the prescribed d ps by approximately 1 nm. Moreover, when comparing one-myosin and multi-myosin systems, the system with more myosin has a larger percentage of the its total elastic potential energy stored within the sarcomere’s internal spring elements (i.e. actin, myosin, titin, bound cross-bridges) as opposed to to the external spring element (i.e. the substrate sarcomere is contracting against), also impacting the ESD ( Fig 6F ).
Results for a (n = 10) showing (A,D) Duty ratio, (B,E) Average force, and (C, D) Plateau ATP consumption rate. Average force and plateau ATP consumption rate are reported as per whole sarcomere. (D) Duty ratio and ATP consumption rate and (E) Average force at standard physiological [ADP][Pi] and varying [ATP] concentrations. (A-E) Standard physiological concentrations for [ATP] and [ADP][Pi] conditions are denoted by the bold red lines ([ATP] = 5 mM, [ADP][Pi] = 0.09 mM 2 ). Dashed white/gray lines represent literature values of [ATP] concentrations where the onset of rigor has been observed experimentally ([ATP] = 0.5 mM) [ 75 , 79 ]. (F) Percent of total elastic potential energy in the spring elements internal to the sarcomere (i.e. actin, myosin, titin, and cross-bridges) and external to the sarcomere (i.e. external spring).
https://doi.org/10.1371/journal.pcbi.1012321.g006
The analytical outputs for a single myosin system ( Fig 7A–7C ) align with the simulation results ( Fig 5C–5E ) if the effective sliding distance, ESD = 6 nm. To accomplish this, we replaced the cross-bridge displacement term ( Table 1 ) in Eqs 9 , 11 – 13 and 16 – 21 as follows: ( x m − x a − b 0 ) = −ESD = − 6 nm. In contrast, the match is not as close when the ESD is assumed to be the same as prescribed: ESD = d ps = 7 nm ( Fig 7D ). This implies that if our hypothesis is correct, smaller ESDs would lead to analytical solutions that mimic the 16-myosin simulation ( Fig 6A ), which was indeed observed at ESD ≈ 3 nm ( Fig 7E ).
(A) Analytically calculated duty ratio ( Eq 16 ) where the power stroke’s effective sliding distance (ESD) = 6 nm. (B) Analytically calculated average force ( Eq 17 ) where ESD = 6 nm. (C) Analytically calculated ATP consumption rate ( Eq 18 ) where ESD = 6 nm. (D) Analytically calculated duty ratio where ESD = d ps = 7 nm, where 7 nm is the power stroke distance against no resistance. This causes an upward and rightward shift in the plot. (E) Analytically calculated duty ratio where ESD = 3 nm. This causes a downward and leftward shift in the plot. (F) Analytically calculated duty ratio where ESD = 6 nm and k ATP ,0 = 7 × 10 −5 s −1 . This causes a rightward shift in the plot. (A-I) Standard physiological concentrations for [ATP] and [ADP][Pi] conditions are denoted by the bold red lines ([ATP] = 5 mM, [ADP][Pi] = 0.09 mM 2 ). Dashed white/gray lines denote the [ATP] concentration associated with the onset of rigor ([ATP] = 0.5 mM) [ 75 , 79 ]. Effect of reducing k ATP ,0 on one-myosin analytical and 16-myosin simulation (n = 10) values for (G) Duty ratio, (H) Average force, and (I) Plateau ATP consumption rate at standard physiological [ADP][Pi] or increased [ADP][Pi] and varying [ATP] concentrations. Reducing k ATP ,0 causes a rightward shift in all of the plots. Increasing environmental [ADP][Pi] by a factor of 10 3 alters 16 myosin system behavior. Average force and plateau ATP consumption rate are reported as per whole sarcomere. (H, inset) The one-myosin analytical system’s predictions of average force compared to muscle strip data (red circles) adapted from White [ 79 ]. Data are normalized to force under complete rigor, at [ATP] = 0.1 μM for the analytical system and [ATP] = 0mM for experimental data.
https://doi.org/10.1371/journal.pcbi.1012321.g007
Although the effective sliding distance cannot be prescribed in a simulation, the phenomena of internal tensions can be manipulated by extending the duration each myosin head remains attached to actin, controlled by adjusting the k ATP ,0 parameter in Eqs 13 and 14 while holding all other parameters as in Table 1 . Indeed, by reducing k ATP ,0 from 10 −2 ] s −1 to 7 × 10 −5 s −1 , we observe a rightward shift in the model’s outputs ( Fig 7F–7I ). A 16-myosin sarcomere simulated with this shift enables the system to exhibit the same average duty ratio among its cross-bridges at physiological [ATP], [ADP][Pi] as a one-myosin system with the original k ATP,0 ( Fig 7G ). Excitingly, this realignment towards a physiological duty ratio is concurrent with the shift in the 16-myosin system’s rigor behavior, matching physiological expectations ( Fig 7G–7I ). A feature exclusive to a shorter ESD system, e.g. the 16-myosin system, is its sensitivity to [ADP][Pi] changes near physiological conditions. For example, if environmental [ADP][Pi] is increased by a factor of 10 3 , there are significant shifts in physiological and rigor associated force outputs and ATP consumption (dashed green line, Fig 7H and 7I ).
A sarcomere is the fundamental unit of muscle contraction, and modeling its behavior can provide insight into the mechanisms of muscle function. The model in this study bridges the gap between stochastic-mechanical sarcomere models and a novel cross-bridge cycle kinetic schema that considers [ATP], [ADP], and [Pi] in their relevant state transitions, conferring it the advantages of both types of models ( Fig 3 ). The rate constant definitions in our model were derived with few underlying assumptions, enabling them to be simpler and more direct than in previous models (Eqs 15 , 6 and 12 ), while also effectively capturing how changes in free energy–and consequently kinetic rates–arise from independent perturbations in either [ATP] or [ADP][Pi].
Utilizing our new kinetic schema, we showed that, for each geometry, as long as the duty ratio remained physiological at standard [ATP], [ADP][Pi] levels, it was possible to predict the concentration at which the onset of rigor is expected (Figs 5C–5F , 7A–7C, 7G–7I ), with the analytical solution agreeing remarkably with experimental data [ 79 ] ( Fig 7H , inset). This approach allowed us to observe how shifts in sarcomere behavior could arise from changes in internal mechanics or kinetic adjustments, demonstrated in this study by varying the effective sliding distance or adjusting the parameter k ATP ,0 . The results suggest that k ATP ,0 is a key parameter in fine-tuning the model’s accuracy and relevance in more complex systems ( Fig 7G–7I ). The backward transition that k ATP ,0 governs may be even lower for 3D systems, whose internal tensions are expected to be even more intricate than our 16-myosin system’s ( Fig 6F and contrasting Fig 6D and 6E with Fig 7G–7I ). Modifying k ATP ,0 to account for internal tensions is consistent with theoretical considerations of cross-bridge cycling under increased internal tensions [ 80 , 81 ] and experimental insights of myosin binding kinetics’ role in muscle function [ 82 ], and is thus a valid means of maintaining model fidelity when investigating increasingly complex muscular systems. Therefore, by simple tuning of the duty ratio, a key feature of this model, the kinetic schema can be applied to studies of different myosin classes and isoforms, conditions characterized by altered muscle energetics, and muscle adaptation to energy stress.
Consistent with the results of our model (Figs 4 – 7 ), it is well documented that a sarcomere’s environmental conditions can lead to increased myosin binding to actin (e.g. low-ATP concentrations, high-ADP concentrations, or rigor conditions) or decreased myosin binding to actin (e.g. high-Pi concentration or myosin inhibitors) [ 83 – 86 ], as is evident in many pathologies [ 1 – 5 ]. Beyond the scale of myosin binding, changes in concentrations of any one of these metabolites has shown varied effects on force metrics of muscle fibers [ 87 – 89 ], in alignment with our results on force output ( Fig 7B and 7H ). Even in non-pathological states, such as during muscle fatigue, [ADP] and [Pi] concentrations can increase significantly (20 to 300-fold and 6 to 10-fold respectively–an increase up to the order of 10 3 in [ADP][Pi] [ 52 , 90 – 94 ]), leading to changes in force output and energetics, which our model can explore ( Fig 7H and 7I ). Taken together, the existence of these conditions where the concentrations of these metabolites move independent from one another necessitates contraction models that are capable of interrogating the effects of imbalances in the [ATP]/[ADP][Pi] ratio based on individual concentrations.
As this model was intentionally made to be simple, it does not include additional intermediate states of the cross-bridge cycle or more complex characteristics of a real sarcomere. For example, according to recent discoveries, the super-relaxed (SRX) state of myosin is important due to its potential role in optimizing sarcomeric energy utilization [ 77 , 95 , 96 ]. Thus, SRX states may need to be included in future iterations of the model as it has been suggested that altered concentrations of environmental [ADP] may cause strain-mediated destabilization of the SRX population in sarcomeres [ 77 , 95 ]. While the phenomenological implementation of this SRX state has been previously modeled [ 24 , 97 ], to include this additional cross-bridge state mechanistically within our model would require more experimental data.
The force traces analyzed in this study observe a half-sarcomere system as it contracts against an external spring, so there is no prescribed velocity of shortening or isotonic shortening ( Fig 4A ). This implementation closely mimics the experimental conditions under which cellular and tissue muscle mechanics are studied, such as in traction force microscopy and muscular thin films [ 59 – 63 ]. Therefore, the model can be paired with “heart-chip” experiments that explore the effect of hypoxia [ 98 ] or other altered [ATP], [ADP], [Pi] conditions to predict reductions in contractility. Similarly, in the future the kinetic schema developed here can be hybridized with prescribed velocity contraction models to explore how power density of the muscle changes with varying [ATP] [ 99 ].
This simple model adequately captured the geometries, mechanics, and kinetics necessary for investigating the chemical and mechanical outputs of sarcomeric force generation while also providing the flexibility to interrogate sarcomeric response to alterations in mechanical and kinetic parameters. The novel approach to the allocation of free energies within this model enabled evaluation of sarcomeric outputs in response to changes in [ATP], [ADP], and [Pi] concentrations that would be otherwise misrepresented. The associated analytical solution for the one-myosin system is a powerful tool to explore how different parameters influence stochastic-mechanical behavior based on how these parameters affect the analytical system. The gained insights not only validate the utility of our model but also establish a solid foundation for future experimental explorations aimed at targeting muscular disorders at a molecular level. Since our model possesses geometric and mechanical elements generally consistent with those of previous models, our novel kinetic schema is an easily integrated augmentation that will lead to this work’s increased relevance as a tool to interrogate energy utilization and force generation of sarcomeres under a variety of ATP, ADP, and Pi environmental conditions.
S1 text. this file contains s1 text sections a–e with details on model derivation, implementation, and parameter exploration, and further citations supporting parameter and method selection..
https://doi.org/10.1371/journal.pcbi.1012321.s001
BY ISABELLA BACKMAN August 5, 2024
Promising new research supports that autoimmunity—in which the immune system targets its own body—may contribute to Long COVID symptoms in some patients.
As covered previously in this blog, researchers have several hypotheses to explain what causes Long COVID, including lingering viral remnants, the reactivation of latent viruses, tissue damage, and autoimmunity.
Now, in a recent study , when researchers gave healthy mice antibodies from patients with Long COVID, some of the animals began showing Long COVID symptoms—specifically heightened pain sensitivity and dizziness. It is among the first studies to offer enticing evidence for the autoimmunity hypothesis. The research was led by Akiko Iwasaki, PhD , Sterling Professor of Immunobiology at Yale School of Medicine (YSM).
“We believe this is a big step forward in trying to understand and provide treatment to patients with this subset of Long COVID,” Iwasaki said.
Iwasaki zeroed in on autoimmunity in this study for several reasons. First, Long COVID’s persistent nature suggested that a chronic triggering of the immune system might be at play. Second, women between ages 30 and 50, who are most susceptible to autoimmune diseases, are also at a heightened risk for Long COVID. Finally, some of Iwasaki’s previous research had detected heightened levels of antibodies in people infected with SARS-CoV-2.
Iwasaki’s team isolated antibodies from blood samples obtained from the Mount Sinai-Yale Long COVID study . They transferred these antibodies into mice and then conducted multiple experiments designed to look for changes in behavior that may indicate the presence of specific symptoms. For many of these experiments, mice that received antibodies [the experimental group] behaved no differently than mice that had not [the control group].
However, a few experiments revealed striking changes in the behavior of the experimental mice. These included:
Among the mice that showed behavioral changes, the researchers identified which patients their antibodies came from and what symptoms they had experienced. Interestingly, of the mice that showed heightened pain, 85% received antibodies from patients that reported pain as one of their Long COVID symptoms. Additionally, 89% of mice that had demonstrated loss of balance and coordination on the rotarod test had received antibodies from patients who reported dizziness. Furthermore, 91% of mice that showed reduced strength and muscle weakness received antibodies from patients who reported headache and 55% from patients who reported tinnitus. More research is needed to better understand this correlation.
The autoimmunity hypothesis has recently been further supported by a research group in the Netherlands led by Jeroen den Dunnen, DRS , associate professor at Amsterdam University Medical Center, which also found a link between patients’ Long COVID antibodies and corresponding symptoms in mice.
Diagnosing and treating Long COVID requires doctors to understand what causes the disease. The new study suggests that treatments targeting autoimmunity, such as B cell depletion therapy or plasmapheresis, might alleviate symptoms in some patients by removing the disease-causing antibodies.
Intravenous immunoglobulin (IVIg) is another therapy used for treating autoimmune diseases like lupus in which patients receive antibodies from healthy donors. While its exact mechanism is still unclear, the treatment can help modulate the immune system and reduce inflammation. Could this treatment help cases of Long COVID that are caused by autoimmunity?
A 2024 study led by Lindsey McAlpine, MD , instructor at YSM and first author, and Serena Spudich, MD , Gilbert H. Glaser Professor of Neurology at YSM and principal investigator, found that IVIg might help improve small fiber neuropathy—a condition associated with numbness or painful sensations in the hands and feet—caused by Long COVID. Iwasaki is hopeful that future clinical trials might reveal the benefits of this treatment in helping some of the other painful symptoms of the diseases.
Other drugs are also in the pipeline, such as FcRn inhibitors. FcRn is a receptor that binds to antibodies and recycles them. Blocking this receptor could help bring down levels of circulating antibodies in the blood. An FcRn receptor was recently approved by the FDA for treating myasthenia gravis, another kind of autoimmune disease.
The study could also help researchers create diagnostic tools for evaluating which patients have Long COVID induced by autoimmunity so that doctors can identify who is most likely to benefit from treatments such as these.
Iwasaki plans to continue researching why and how autoantibodies might cause Long COVID, as well as conduct randomized clinical trials on promising treatments. She is also conducting similar antibody transfer studies in other post-acute infection syndromes, such as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).
In the meantime, she is excited about her team’s promising results. “Seeing this one-to-one correlation of antibodies that cause pain from patients who reported pain is really gratifying to me as it suggests a causal link,” she says. “It’s a first step, but I think it’s a big one.”
Isabella Backman is associate editor and writer at Yale School of Medicine.
I am very excited by this research, which suggests that at least some of the symptoms of Long COVID are driven by autoimmunity. If so, then this suggests that there may be a way to test for some versions of Long COVID. And if we could identify the patients who have an autoimmune-driven disease, we have treatments to try that have been used with success in other autoimmune diseases. Many of the autoimmune diseases are treated with medications that suppress the immune system. These are powerful medicines that can leave an individual at risk for infection, so they must be thoughtfully applied to patients with evidence of immune system involvement.
I feel as though every blog post here ends with the possibility of better testing and better treatment, but what makes this different is that it points in a very specific direction and leads to the kind of specific questions that help get to useful answers. Which antibodies are involved? Which cells? And finally, can we develop treatments that are specific to those antibodies or to their targets? These are exciting questions, which will, I hope, lead to useful answers.
Read other installments of Long COVID Dispatches here .
If you’d like to share your experience with Long COVID for possible use in a future post (under a pseudonym), write to us at: [email protected]
Information provided in Yale Medicine content is for general informational purposes only. It should never be used as a substitute for medical advice from your doctor or other qualified clinician. Always seek the individual advice of your health care provider for any questions you have regarding a medical condition.
Covering atomic, molecular, and optical physics and quantum science.
Jan lennart bönsel, satoya imai, ye-chao liu, and otfried gühne, phys. rev. a 110 , 022410 – published 7 august 2024.
How can we analyze quantum correlations in large and noisy systems without quantum state tomography? An established method is to measure total angular momenta and employ the so-called spin-squeezing inequalities based on their expectations and variances. This allows detection of metrologically useful entanglement, but efficient strategies for estimating such nonlinear quantities have yet to be determined. In this paper we show that spin-squeezing inequalities can not only be evaluated by measurements of the total angular momentum but also by two-qubit correlations, either involving all pair correlations or randomly chosen pair correlations. Then we analyze the estimation errors of our approaches in terms of a hypothesis test. For this purpose, we discuss how error bounds can be derived for nonlinear estimators with the help of their variances, characterizing the probability of falsely detecting a separable state as entangled. We focus on the spin-squeezing inequalities in multiqubit systems. Our methods, however, can also be applied to spin-squeezing inequalities for qudits or for the statistical treatment of other nonlinear parameters of quantum states.
DOI: https://doi.org/10.1103/PhysRevA.110.022410
©2024 American Physical Society
References (subscription required).
Vol. 110, Iss. 2 — August 2024
Other options.
Visualization of the singlet state | Ψ − 〉 (red) and the Dicke state | D N , N / 2 〉 (blue) on the collective Bloch sphere [ 40 ]. Singlet states are characterized by vanishing mean spin 〈 J ⃗ 〉 = 0 and variances. Hence, the singlet state | Ψ − 〉 corresponds to the red dot at the origin. The Dicke state | D N , N / 2 〉 is also at the origin, though it has a nonzero variance in the x − y plane that is shown by the blue shaded area.
Upper bound of the p value. The plot shows an exemplary probability density function f ξ ̃ of the estimator for a separable state with spin-squeezing parameter ξ = ξ s . ξ s denotes the extremal value that can be achieved by separable states. To observe an outcome ξ 1 , the estimator has to deviate at least by t = ξ 1 − ξ s from its mean. The probability P ( ξ ̃ − ξ ≥ t ) for this to happen corresponds to the red area.
Measurement scheme for the estimators 〈 J α 2 〉 ̃ TS and ( Δ J α ) 2 ̃ TS . In each repetition k , the total spin of the system is measured. In an ion trap, this can be done by resonance fluorescence [ 34 ], which also gives access to the spin of the individual qubits. The figure includes an image of trapped 171 Yb + ions, which is reprinted from [ 34 ].
Measurement pattern for (a) 〈 J α 2 〉 ̃ AP in Eq. ( 20 ) as well as ( Δ J α ) 2 ̃ AP in Eq. ( 21 ) and (b) 〈 J α 〉 2 ̃ AP in Eq. ( 23 ). In pattern (a) all N ( N − 1 ) distinct pairs of qubits are measured K AP times. In contrast, in pattern (b) all N 2 pairs are measured, with each qubit observed only in K AP 2 of the experimental runs to ensure statistical independence. The approach AP1 relies only on the measurement pattern (a), whereas for AP2 both the patterns (a) and (b) are used.
Measurement pattern for (a) 〈 J α 2 〉 ̃ RP in Eq. ( 25 ) and ( Δ J α ) 2 ̃ RP in Eq. ( 27 ) and for (b) 〈 J α 〉 2 ̃ RP in Eq. ( 29 ). In pattern (a), L RP random pair correlations are measured K RP -times each. Pattern (b) in turn uses also L RP random pairs ( i , j ) , but with the possibility that i = j . In K RP 2 of the repetitions qubit i is measured, whereas in the other repetitions qubit j is observed. The scheme RP1 is only based on the pattern (a), whereas RP2 relies on both patterns (a) and (b).
Probability distribution of the estimator ( ξ ̃ c ) TS . The simulation has been performed for the 10-qubit Dicke state | D 10 , 5 〉 defined in Eq. ( 9 ) with K TS = 7400 . The histogram contains 99 bins, but due to the small bin size of 0.02 they are not well resolved.
Probability distribution of the estimator ( ξ ̃ c ) RP1 . The simulation has been performed for the 10-qubit Dicke state | D 10 , 5 〉 . L RP1 = 7400 random pairs have been chosen with K RP1 = 1 repetitions. The histogram consists of 99 bins with a size of 0.2.
Variances of the estimators ( ξ ̃ c ) TS , ( ξ ̃ c ) AP1 , ( ξ ̃ c ) AP2 , ( ξ ̃ c ) RP1 , and ( ξ ̃ c ) RP2 for the Dicke state of N = 10 qubits | D 10 , 5 〉 mixed with depolarization noise, i.e., ρ = p | D 10 , 5 〉 〈 D 10 , 5 | + ( 1 − p ) 1 / 2 N . The variances are obtained for K TS = 7400 , K AP1 = 82 , K AP2 = 60 , L RP1 = 7400 with K RP1 = 1 and L RP2 = 2775 with K RP2 = 2 .
Number of state preparations necessary to verify a violation of Eq. ( 6c ) by t = 0.1 × N 2 with a significance level of γ = 0.95 .
Sign up to receive regular email alerts from Physical Review A
Paste a citation or doi, enter a citation.
No.Name |
---|
1 |
3 |
14 |
2 6 |
12 |
17 16 |
5 |
13 7 |
15 11 |
9 4 |
10 |
Substitutes |
---|
18 |
20 |
Giulia Gwinn |
Janina Minge |
Sydney Lohmann |
Feli Rauch |
Ann-Katrin Berger |
Match commentary.
2024 olympic games women's soccer: bracket, fixtures schedule, surviving group of death will have prepared japan for huge quarterfinal test against uswnt, gustavsson exits matildas after olympic ko.
Advertisement
The law, which was passed in Minnesota last year, includes language requiring menstrual products to be available in bathrooms of all schools for grades 4 to 12 as a way to accommodate transgender students.
By Chris Cameron
As part of their effort to portray Tim Walz, the new Democratic vice-presidential candidate, as a far-left liberal, the Trump campaign attacked the Minnesota governor on Tuesday for signing a bill last year that provides access to menstrual products for transgender students.
At issue is broadly inclusive language in the law, which states that products like pads, tampons and other products used for menstruation “must be available to all menstruating students in restrooms regularly used by students in grades 4 to 12.” Republican state lawmakers in Minnesota had tried — and failed — to amend that bill so that it would apply only to “female restrooms,” though some Republicans went on to vote for the final version of the bill .
Karoline Leavitt, a spokeswoman for the Trump campaign, said in an interview on Tuesday on Fox News that the law, among other policies seen as supportive of transgender rights, was “a threat to women’s health.”
“As a woman, I think there is no greater threat to our health than leaders who support gender-transition surgeries for young minors , who support putting tampons in men’s bathrooms in public schools,” Ms. Leavitt said. “Those are radical policies that Tim Walz supports. He actually signed a bill to do that.”
State Representative Sandra Feist , a Democrat and the chief author of the bill, said in an interview that it was important for her and the student activists who pushed for the change that transgender students were able to access menstrual products without having to ask for them.
“I actually received emails,” Ms. Feist said. “From trans students, parents, teachers, librarians, custodians from across the country, talking about how they were — or that they knew — trans students who faced these barriers and needed these products, and how much it meant to them that they would have that access, and also that we were standing up for them.”
Mr. Walz made significant efforts to protect the rights of L.G.B.T.Q. people in Minnesota as governor, and was an early supporter of gay rights going as far back as his time as a high school teacher in the 1990s. Mr. Walz signed a bill last year designating Minnesota as a legal refuge for transgender people.
Chris Cameron covers politics for The Times, focusing on breaking news and the 2024 campaign. More about Chris Cameron
COMMENTS
Table of contents. Step 1: State your null and alternate hypothesis. Step 2: Collect data. Step 3: Perform a statistical test. Step 4: Decide whether to reject or fail to reject your null hypothesis. Step 5: Present your findings. Other interesting articles. Frequently asked questions about hypothesis testing.
In hypothesis testing, the goal is to see if there is sufficient statistical evidence to reject a presumed null hypothesis in favor of a conjectured alternative hypothesis.The null hypothesis is usually denoted \(H_0\) while the alternative hypothesis is usually denoted \(H_1\). An hypothesis test is a statistical decision; the conclusion will either be to reject the null hypothesis in favor ...
Hypothesis testing is a crucial procedure to perform when you want to make inferences about a population using a random sample. These inferences include estimating population properties such as the mean, differences between means, proportions, and the relationships between variables. This post provides an overview of statistical hypothesis testing.
The researchers write their hypotheses. These statements apply to the population, so they use the mu (μ) symbol for the population mean parameter.. Null Hypothesis (H 0): The population means of the test scores for the two groups are equal (μ 1 = μ 2).; Alternative Hypothesis (H A): The population means of the test scores for the two groups are unequal (μ 1 ≠ μ 2).
The first step in hypothesis testing is to set up two competing hypotheses. The hypotheses are the most important aspect. If the hypotheses are incorrect, your conclusion will also be incorrect. The two hypotheses are named the null hypothesis and the alternative hypothesis. The null hypothesis is typically denoted as H 0.
Hypothesis testing is an essential procedure in statistics. A hypothesis test evaluates two mutually exclusive statements about a population to determine which statement is best supported by the sample data. When we say that a finding is statistically significant, it's thanks to a hypothesis test. ... Our goal is to determine whether our ...
Explore the intricacies of hypothesis testing, a cornerstone of statistical analysis. Dive into methods, interpretations, and applications for making data-driven decisions. In this Blog post we will learn: What is Hypothesis Testing? Steps in Hypothesis Testing 2.1. Set up Hypotheses: Null and Alternative 2.2. Choose a Significance Level (α) 2.3.
Hypothesis Testing Step 1: State the Hypotheses. In all three examples, our aim is to decide between two opposing points of view, Claim 1 and Claim 2. In hypothesis testing, Claim 1 is called the null hypothesis (denoted " Ho "), and Claim 2 plays the role of the alternative hypothesis (denoted " Ha ").
8.2 FOUR STEPS TO HYPOTHESIS TESTING The goal of hypothesis testing is to determine the likelihood that a population parameter, such as the mean, is likely to be true. In this section, we describe the four steps of hypothesis testing that were briefly introduced in Section 8.1: Step 1: State the hypotheses. Step 2: Set the criteria for a decision.
A hypothesis test consists of five steps: 1. State the hypotheses. State the null and alternative hypotheses. These two hypotheses need to be mutually exclusive, so if one is true then the other must be false. 2. Determine a significance level to use for the hypothesis. Decide on a significance level.
Testing the Null Hypothesis. The primary goal of a statistical test is to determine whether an observed data set is so different from what you would expect under the null hypothesis that you should reject the null hypothesis. For example, let's say you are studying sex determination in chickens. For breeds of chickens that are bred to lay lots ...
Below these are summarized into six such steps to conducting a test of a hypothesis. Set up the hypotheses and check conditions: Each hypothesis test includes two hypotheses about the population. One is the null hypothesis, notated as H 0, which is a statement of a particular parameter value. This hypothesis is assumed to be true until there is ...
Mean Population IQ: 100. Step 1: Using the value of the mean population IQ, we establish the null hypothesis as 100. Step 2: State that the alternative hypothesis is greater than 100. Step 3: State the alpha level as 0.05 or 5%. Step 4: Find the rejection region area (given by your alpha level above) from the z-table.
Hypothesis testing is a technique that is used to verify whether the results of an experiment are statistically significant. It involves the setting up of a null hypothesis and an alternate hypothesis. There are three types of tests that can be conducted under hypothesis testing - z test, t test, and chi square test.
Unit test. Significance tests give us a formal process for using sample data to evaluate the likelihood of some claim about a population value. Learn how to conduct significance tests and calculate p-values to see how likely a sample result is to occur by random chance. You'll also see how we use p-values to make conclusions about hypotheses.
Hypothesis testing. Hypothesis testing is a formal process of statistical analysis using inferential statistics. The goal of hypothesis testing is to compare populations or assess relationships between variables using samples. Hypotheses, or predictions, are tested using statistical tests. Statistical tests also estimate sampling errors so that ...
Hypothesis testing is a systematic procedure for deciding whether the results of a research study support a particular theory which applies to a population. ... The purpose of hypothesis testing is to test whether the null hypothesis (there is no difference, no effect) can be rejected or approved. If the null hypothesis is rejected, then the ...
Hypothesis testing is a statistical method used to determine if there is enough evidence in a sample data to draw conclusions about a population. It involves formulating two competing hypotheses, the null hypothesis (H0) and the alternative hypothesis (Ha), and then collecting data to assess the evidence.
Hypothesis testing is an act in statistics whereby an analyst tests an assumption regarding a population parameter. The methodology employed by the analyst depends on the nature of the data used ...
Testing the hypothesis: Step 2 (Set an acceptable level of risk, referred to as the alpha level) When testing a research hypothesis, 4 possible outcomes or decisions: 1) null hypothesis is accepted when it is true (correct decision); 2) null hypothesis is rejected when it is false (correct decision); accepting alternative hypothesis.
Examples of Hypothesis. Here are a few examples of hypotheses in different fields: Psychology: "Increased exposure to violent video games leads to increased aggressive behavior in adolescents.". Biology: "Higher levels of carbon dioxide in the atmosphere will lead to increased plant growth.".
The goal of statistical testing is to decide whether there is sufficient evidence from the sample under study to conclude that the alternative hypothesis should be believed. Hypothesis testing has been likened to a criminal trial, in which a jury must use evidence to decide which of 2 possible truths, innocence (H 0 ) or guilt (H A ), is to be ...
Based from the z-score that you have generated, what should be your decision for the hypothesis test? i. Reject the null hypothesis as the z-test statistic is greater than the z-score of a 95% confidence level (+1.96). ii. Reject the null hypothesis as the z-test statistic is less than the z-score of a 95% confidence level (+1.96). iii.
It's a hypothesis worth considering because, if you haven't noticed, chicken sucks. It's boring. The amount of attention necessary to inject the faintest whiff of dynamism into the bird has ...
To test this hypothesis, we constructed a stochastic-mechanical half-sarcomere model whose kinetics explicitly account for the fact that ATP and ADP/Pi interact with myosin at different times in the cross-bridge cycle. ... The goal for this model was to include the simplest chemo-mechanical dynamics necessary to investigate the effect of the ...
The autoimmunity hypothesis has recently been further supported by a research group in the Netherlands led by Jeroen den Dunnen, DRS, associate professor at Amsterdam University Medical Center, which also found a link between patients' Long COVID antibodies and corresponding symptoms in mice.
How can we analyze quantum correlations in large and noisy systems without quantum state tomography? An established method is to measure total angular momenta and employ the so-called spin-squeezing inequalities based on their expectations and variances. This allows detection of metrologically useful entanglement, but efficient strategies for estimating such nonlinear quantities have yet to be ...
The important thing to recognize is that the goal of a hypothesis test is not to show that the research hypothesis is (probably) true; the goal is to show that the null hypothesis is (probably) false. Most people find this pretty weird. The best way to think about it, in my experience, is to imagine that a hypothesis test is a criminal trial…
Game summary of the Germany vs. Canada Women's Olympic Soccer Tournament game, final score 0-0, from August 3, 2024 on ESPN.
The law, which was passed in Minnesota last year, includes language requiring menstrual products to be available in bathrooms of all schools for grades 4 to 12 as a way to accommodate transgender ...