(Press-News.org) Computer simulations help materials scientists and biochemists study the motion of macromolecules, advancing the development of new drugs and sustainable materials. However, these simulations pose a challenge for even the most powerful supercomputers.
A University of Oregon graduate student has developed a new mathematical equation that significantly improves the accuracy of the simplified computer models used to study the motion and behavior of large molecules such as proteins, nucleic acids and synthetic materials such as plastics.
The breakthrough, published last month in Physical Review Letters, enhances researchers’ ability to investigate the motion of large molecules in complex biological processes, such as DNA replication. It could aid in understanding diseases linked to errors in such replication, potentially leading to new diagnostic and therapeutic strategies.
“We want to understand how molecules move, twist and function,” said Jesse Hall, a physics doctoral candidate who worked with theoretical physical chemistry professor Marina Guenza to develop the new model. “With this new equation, we can simulate larger protein complexes and gain deeper insight into how these molecular machines work in the body.”
Hall’s research has made progress on a problem computational scientists have been working on for more than 50 years: how to accurately calculate the friction biomolecules experience within their chaotic, viscous environment.
Biomolecules — molecules produced by a living organism, such as proteins — are surrounded by thousands of water molecules, along with other proteins, nucleic acids and other types of molecules. Within this environment, they’re in constant motion; they fold, unfold and bind to nucleic acids and other proteins.
“They’re wriggling around in there, and the mechanics of what they do is very important for understanding how DNA replication works or developing drugs to target a certain mechanism,” Hall said.
Rather than synthesizing physical samples to study, scientists use computer models as a virtual lab. That allows them to alter the molecules they’re analyzing by modifying their code so they can then study the effects of the change.
“When you have a good, coarse-grained model, you can simulate large systems,” said Guenza, who is co-author of the study. “For example, one can see how molecules move together, rearrange, combine and function as a machine. You can change one amino acid and see how the mutation affects the way the molecules perform their biological function.”
Because biomolecular systems are so large and complex, researchers rely on coarse-grained mathematical models, which simulate molecular movements without having to depict each individual atom. That helps keep computing costs down while speeding up computation.
But scientists have struggled for decades to accurately calculate the value of friction, which is part of the data used when running coarse-grained simulations, Guenza said.
As molecules move through fluid, the resulting friction creates a drag effect, affecting both their internal fluctuations and their external movements.
"To describe how a protein moves, you have to balance the different forces: the viscous forces, the random forces from collision with surrounding molecules, and the internal forces that keep the molecule together,” Guenza said.
Other researchers have devised mathematical solutions starting from a formula known as the “Einstein relation,” which establishes the relationship between a particle’s diffusion, or how quickly it spreads out, and its mobility, or how easily it can be moved. But those solutions have their limits.
“There’s a lot of good work out there for describing one aspect of a protein’s motion, but we need more complete models that can describe several aspects of a protein’s motion at once,” Hall said. “We’ve basically come up with a much more general form of the Einstein relation, which offers a lot more choice and freedom. It allows us to flexibly tune our calculations to a specific system and get more reliable results.”
Hall’s equation is the first to simultaneously describe friction for both a molecule’s internal fluctuations and its external diffusion through the fluid, Guenza said.
“This is a brilliant solution,” she said. “Jesse’s work provides a highly accurate tool that can be applied to both simple and complex molecular systems, making simulations of these large systems both faster and more accurate.”
For many years, the Guenza group has focused on developing accurate theoretical tools that accelerate molecular simulations, tools that are essential for designing new polymer-based materials and for studying how proteins interact with DNA during replication. Errors in DNA replication play a role in the development of cancer and can lead to a broad range of genetic disorders.
“We realized we needed to build some more tools to get really accurate, precise mathematical models,” Hall said.
Although his research is primarily theoretical, “we’re building toward some more practical tools we can use later,” Hall said. “Hopefully this is a tool that other people can use to work on projects that never even would have occurred to me.”
END
UO researcher develops new tool that could aid drug development
The advance helps scientists better simulate the behavior of proteins and other biological molecules
2025-05-09
ELSE PRESS RELEASES FROM THIS DATE:
Call for abstracts: GSA Connects 2025 invites geoscientists to share groundbreaking research
2025-05-09
FOR IMMEDIATE RELEASE
9 May 2025
The Geological Society of America
Release No. 25-06
Contact: Katie Busser
+1-303-357-1044
kbusser@geosociety.org
Boulder, Colo., USA: The Geological Society of America (GSA) invites scientists, researchers, and professionals from across the globe to submit abstracts for its annual meeting, GSA Connects 2025, taking place 19–22 October 2025 in San Antonio, Texas, USA.
Held annually, GSA Connects is one of the premier international gatherings in the geoscience community, offering a dynamic platform for sharing cutting-edge research and fostering interdisciplinary dialogue. This year’s meeting ...
The skinny on fat, ascites and anti-tumor immunity
2025-05-09
MAY 9, 2025, NEW YORK – A Ludwig Cancer Research study has identified a key mechanism by which advanced ovarian cancers suppress anti-tumor immune responses and resist immunotherapies. Led by Ludwig Princeton’s Lydia Lynch and reported in the current issue of Science Immunology, the study details how ascites fluid—produced in large quantities as ovarian cancer spreads from the ovaries into the abdomen and its organs—sabotages cytotoxic lymphocytes, a class of immune cells that kill cancer cells.
“Although ascites fluid has long been known to be immunosuppressive, it has not been clear what precisely gives it that property,” explained Lynch. “We discovered ...
New film series 'The Deadly Five' highlights global animal infectious diseases
2025-05-09
The EU-funded WiLiMan-ID project (https://www.wiliman-id.eu/) is excited to announce the launch of a brand-new short film series, The Deadly Five. This series is aimed at raising awareness of five critical animal infectious diseases, classified as high priority. Each film in the series focuses on a different disease and the experts studying and fighting them, highlighting the risks each disease poses to animal and public health, as well as the strategies being developed to mitigate their impact.
“Through this series, we aim at bringing ...
Four organizations receive funds to combat food insecurity
2025-05-09
DALLAS, May 7, 2025 — One in eight U.S. households struggles to access enough food, and that number is on the rise.[1] The American Heart Association is building on its 100 years of lifesaving service to fund social enterprises to sustainably improve this driver of health and change the future of health for all.
To that end, the Bernard J. Tyson Impact Fund, part of American Heart Association Ventures’ Social Impact Funds, is distributing $900,000 to four organizations:
Attane Health, based in Kansas City, Missouri, provides access to personalized, nutritious groceries and educational resources for those living with chronic health conditions;
Farm Generations Cooperative, ...
Ultrasound unlocks a safer, greener way to make hydrogels
2025-05-09
Researchers at McGill University, in collaboration with Polytechnique Montréal, pioneered a new way to create hydrogels using ultrasound, eliminating the need for toxic chemical initiators. This breakthrough offers a faster, cleaner and more sustainable approach to hydrogel fabrication, and produces hydrogels that are stronger, more flexible and highly resistant to freezing and dehydration. The new method also promises to facilitate advances in tissue engineering, bioadhesives and 3D bioprinting.
Hydrogels are gels composed of polymers ...
Antibiotics from human use are contaminating rivers worldwide, study shows
2025-05-09
Millions of kilometres of rivers around the world are carrying antibiotic pollution at levels high enough to promote drug resistance and harm aquatic life, a McGill University-led study warns.
Published in PNAS Nexus, the study is the first to estimate the scale of global river contamination from human antibiotics use. Researchers calculated that about 8,500 tonnes of antibiotics – nearly one-third of what people consume annually – end up in river systems around the world each year even after in many cases ...
A more realistic look at DNA in action
2025-05-09
Most scientists look at DNA behavior in isolation, without considering how matter within a cell interacts with DNA
Researchers observed DNA strand separation preceding replication and repair suppressed by molecules pushing strands together
Findings challenge the standard in biochemical practice of heating DNA to separate strands
EVANSTON, Ill. --- By creating a more true-to-life representation of DNA’s environment, researchers at Northwestern University have discovered that strand separation — the essential process a “resting” double helix undergoes before it can initiate replication or make repairs — may take more mechanical force ...
Skia: Shedding light on shadow branches
2025-05-09
What happens when trailblazing engineers and industry professionals team up? The answer may transform the future of computing efficiency for modern data centers.
Data centers house and use large computers to run massive amounts of data. Oftentimes, the processors can’t keep up with this workload because it’s taxing to predict and prepare instructions to carry out. This slows the flow of data. Thus, when you type a question into a search engine, the answer generates more slowly or doesn’t provide the information you need.
To remedy this issue, researchers at Texas ...
Fat-rich fluid fuels immune failure in ovarian cancer
2025-05-09
New research led by Irish scientists has uncovered how lipid-rich fluid in the abdomen, known as ascites, plays a central role in weakening the body’s immune response in advanced ovarian cancer. The findings offer new insights into immune suppression in ovarian cancer and open promising avenues for future immunotherapy approaches.
Over 70% of patients with ovarian cancer are diagnosed at an advanced stage, often presenting with large volumes of ascites. This ascites fluid not only supports the spread of cancer throughout the abdominal cavity but also ...
The origins of language
2025-05-09
To the point
Chimpanzees are capable of complex communication: The human capacity for language may not be as unique as previously thought. Chimpanzees have a complex communication system that allows them to combine calls to create new meanings, similar to human language.
Combining calls creatively: Chimpanzees use four ways to change meaning when combining single calls into two-call combinations, including compositional and non-compositional combinations, and they use a large variety of call combinations in a wide range of contexts.
Origins of language: The discovery of a complex communication system in chimpanzees has important ...
LAST 30 PRESS RELEASES:
Scientists target ‘molecular machine’ in the war against antimicrobial resistance
Extending classical CNOP method for deep-learning atmospheric and oceanic forecasting
Aston University research: Parents should encourage structure and independence around food to support children’s healthy eating
Thunderstorms are a major driver of tree death in tropical forests
Danforth Plant Science Center adds two new faculty members
Robotic eyes mimic human vision for superfast response to extreme lighting
Racial inequities and access to COVID-19 treatment
Residential segregation and lung cancer risk in African American adults
Scientists wipe out aggressive brain cancer tumors by targeting cellular ‘motors’
Capturability distinction analysis of continuous and pulsed guidance laws
CHEST expands Bridging Specialties Initiative to include NTM disease and bronchiectasis on World Bronchiectasis Day
Exposure to air pollution may cause heart damage
SwRI, UTSA selected by NASA to test electrolyzer technology aboard parabolic flight
Prebiotics might be a factor in preventing or treating issues caused by low brain GABA
Youngest in class at higher risk of mental health problems
American Heart Association announces new volunteer leaders for 2025-26
Gut microbiota analysis can help catch gestational diabetes
FAU’s Paulina DeVito awarded prestigious NSF Graduate Research Fellowship
Champions for change – Paid time off initiative just made clinical trials participation easier
Fentanyl detection through packaging
Prof. Eran Meshorer elected to EMBO for pioneering work in epigenetics
New 3D glacier visualizations provide insights into a hotter Earth
Creativity across disciplines
Consequences of low Antarctic sea ice
Hear here: How loudness and acoustic cues help us judge where a speaker is facing
A unique method of rare-earth recycling can strengthen the raw material independence of Europe and America
Epilepsy self-management program shows promise to control seizures, improve mood and quality of life
Fat may play an important role in brain metabolism
New study finds no lasting impact of pandemic pet ownership on human well-being
New insights on genetic damage of some chemotherapies could guide future treatments with less harmful side effects
[Press-News.org] UO researcher develops new tool that could aid drug developmentThe advance helps scientists better simulate the behavior of proteins and other biological molecules