Coarse-grained Modelling Professors and Supervisors

Jiali Gaoمشاهده پروفایل

استاد

University of Minnesota Twin CitiesUnited States

Professor Jiali Gao is a faculty member in the Department of Chemistry at the University of Minnesota, where he holds the position of Professor. His research program focuses on developing computational methods to study complex biological systems through the integration of quantum mechanics and molecular mechanics (QM/MM) approaches. Professor Gao's research interests span multiple interconnected areas: Development of novel combined QM/MM methods for studying chemical and biological reactions Understanding the physical origins of enzyme catalysis Modeling diffusion and interactions of macromolecular particles in cellular environments Application of computational methods to energy-related problems including photosynthesis and combustion His recent publications demonstrate a consistent focus on advancing computational methodologies while applying them to significant biological and chemical problems. Professor Gao's work bridges theoretical development with practical applications across multiple domains including protein dynamics, spectroscopy, and reaction mechanisms. Notable contributions include the development of the CARNOT simulation package for reactive systems and significant advances in multistate density functional theory. Professor Gao maintains an active research program with numerous publications each year in high-impact journals such as Nature Communications, Journal of Chemical Physics, and Journal of Chemical Theory and Computation. His interdisciplinary approach, connecting computational and experimental work, strengthens the impact of his research by providing molecular-level interpretations of experimental observations.

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Henryk Krawczykمشاهده پروفایل

استاد

Gdańsk University of TechnologyPoland

prof. dr hab. inż. Henryk Krawczyk serves as a Professor at Gdańsk University of Technology within the Faculty of Electronics, Telecommunications and Informatics. He is based at the Task Computing Centre (Centrum Informatyczne Task) in the Building of Electronics, Telecommunications and Informatics (room 520), with contact email hkrawk@pg.edu.pl and phone 583471018. His research spans critical intersections of cloud infrastructure and computational intelligence: Intelligent cloud service engineering with resilience-focused development frameworks Rural IoT deployment solutions for underserved telecommunications environments Machine learning optimization for constrained edge devices GPU-accelerated computational biology simulations DevOps/CI/CD integration in cloud service lifecycles Analysis of his 2024-2025 publications reveals a strategic emphasis on practical implementations where cloud platforms bridge theoretical AI advances with real-world engineering challenges. His work particularly addresses infrastructure limitations in rural IoT deployment through intelligent data cleaning mechanisms and develops quality assessment metrics for next-generation cloud services. The protein simulation research demonstrates cross-disciplinary application of high-performance computing techniques. As a core member of Gdańsk Tech's Task Computing Centre, Professor Krawczyk leverages institutional high-performance computing resources to advance scalable cloud architectures and computational biology methodologies. No information regarding student supervision or research grants was provided in available materials.

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Niny Z. Raoمشاهده پروفایل

دانشیار

Thomas Jefferson UniversityUnited States

Niny Z. Rao serves as Associate Professor in the Department of Chemistry within the College of Life Sciences at Thomas Jefferson University, Philadelphia, PA. Her academic appointments and research activities are centered at this institution with laboratory facilities in the Chemistry division. Her educational foundation includes: PhD in Physical Chemistry from Florida State University (2002) BChE from The Cooper Union for the Advancement of Science and Art (1998) Dr. Rao's research program spans two distinct yet complementary domains: computational chemistry and artisanal food/beverage chemistry . In computational chemistry, she employs quantum mechanical methods to characterize molecular structures and properties relevant to materials science and medicinal chemistry. Her food chemistry work focuses on traditional production methods, particularly investigating how roasting parameters and brewing techniques alter chemical profiles in artisanal coffee. Current projects emphasize cold brew coffee chemistry, examining variables like contact time, roast levels, and bean varieties to understand antioxidant extraction and flavor compound stability. This dual focus bridges theoretical molecular science with practical food chemistry applications. Analysis of her publication record reveals strong concentration in coffee chemistry (8 of 15 recent articles), particularly cold brew optimization and spent coffee valorization. The remaining publications demonstrate deep expertise in computational chemistry, including boron-containing compounds, polyene systems, and biomolecular simulations. This pattern indicates strategic focus on applied food chemistry while maintaining foundational computational research capabilities. Dr. Rao actively mentors undergraduate researchers through Jefferson's research program, with student projects frequently presented at regional and national conferences. Her supervision emphasizes hands-on analytical techniques and computational modeling, preparing students for advanced scientific careers. While no major research grants are explicitly mentioned, her consistent publication output suggests sustained funding support for laboratory operations and student stipends. Her laboratory work integrates analytical chemistry instrumentation for coffee analysis with computational resources for quantum chemical calculations, creating a hybrid research environment that bridges experimental and theoretical approaches to chemical problems.

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Emil Thomasenمشاهده پروفایل

پژوهشگر

University of CopenhagenDenmark

Emil Thomasen serves as a Guest Researcher in the Department of Biology within the Biomolecular Sciences unit at the University of Copenhagen's Faculty of Science. His research integrates computational methods with experimental structural biology approaches to investigate complex biomolecular systems. Position: Guest Researcher Institution: University of Copenhagen Department: Department of Biology Research Unit: Biomolecular Sciences Contact: fe.thomasen@bio.ku.dk | +4535323586 Thomasen's research focuses on developing and applying computational methodologies to understand protein structure, dynamics, and interactions. His work bridges quantum mechanics, molecular dynamics simulations, and experimental techniques including small-angle X-ray scattering (SAXS) and cryo-electron microscopy. He has made significant contributions to coarse-grained modeling, particularly with the Martini force field, and has pioneered approaches combining machine learning with quantum mechanical calculations for large molecular assemblies. His publication record demonstrates a clear trajectory in computational structural biology, with recent work emphasizing the integration of multiple experimental and computational techniques to characterize complex protein systems. The research shows increasing sophistication in handling large-scale biomolecular assemblies and applying advanced statistical methods like Bayesian inference for model refinement. Thomasen has established strong collaborative networks, frequently working with Professor K. Lindorff-Larsen and other researchers across computational chemistry and structural biology disciplines. His work has appeared in high-impact journals including Nature Communications, eLife, and Journal of Chemical Theory and Computation. As a recently completed Ph.D. graduate (2024), Thomasen continues to advance his research program as a Guest Researcher, building on his doctoral work focused on integrating coarse-grained molecular dynamics with SAXS data for characterizing multidomain protein assemblies.

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Wylie Strobergمشاهده پروفایل

استادیار

University of AlbertaCanada

Wylie Stroberg is an Assistant Professor in the Department of Mechanical Engineering within the Faculty of Engineering at the University of Alberta. He leads the Computational BioSystems Lab, where he conducts research at the interface between cell biology, physiology and engineering using a range of computational and theoretical techniques. His research interests span multiple areas including: Biomechanics and Biomedical Engineering Biomaterials Mechanics and Materials Composites and Polymers Nano and Micro Materials Computational Mechanics Systems Biology of Proteostasis and the Unfolded Protein Response Reactions in Crowded Cellular Compartments Wetting Phenomena of Nanoscale Structures Dr. Stroberg's research focuses on developing new quantitative techniques for studying complex biological systems across disparate length and time scales. His work has significant implications for understanding cellular physiology, protein homeostasis, and developing new therapeutic approaches for age-associated and protein folding diseases. He employs advanced computational methods including multiscale modeling, machine learning, and theoretical analysis to investigate biological phenomena from the molecular to cellular level. His research group has published extensively in mathematical biology and computational mechanics, with a consistent focus on enzyme kinetics, cellular stress responses, and computational modeling of biological processes. The publications demonstrate a strong interdisciplinary approach combining techniques from mechanical engineering, computational science, and molecular biology. Dr. Stroberg has received recognition for his work in mathematical biology and systems biology, with publications in journals such as the Journal of Theoretical Biology, Biophysical Journal, and Mathematical Biosciences. He currently advises several graduate students working on diverse projects including multiscale modeling of enzymatic nanosensors, protein-based modulation of endoplasmic reticulum shape, development of machine learning-based coarse grained models for high-entropy alloys, and simulation of high-entropy alloys for thermal-spray deposition. His lab has trained undergraduate and master's students who have gone on to further academic pursuits. The Computational BioSystems Lab maintains active collaborations with other researchers at the University of Alberta and beyond, working at the intersection of engineering, biology, and computational science.

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Robinson Cortes-Huertoمشاهده پروفایل

استاد پژوهشی

Max Planck Institute for Polymer ResearchGermany

Dr. Robinson Cortes-Huerto serves as Group Leader at the Max Planck Institute for Polymer Research (MPI-P) in Mainz since 2019, leading research in advanced molecular simulation methodologies within Prof. Kurt Kremer's department. His position represents a senior research-focused academic role equivalent to Research Professor in the German Max Planck system. His educational trajectory includes: Bachelor's and Master's degrees in Physics from Universidad Nacional de Colombia, Bogotá Doctorate (2010) from Queen's University Belfast under Prof. Pietro Ballone Postdoctoral research at CINaM-Marseille, INSP-Paris, and CEA-Saclay Research expertise centers on developing the adaptive solution method for free energy calculations and non-equilibrium molecular dynamics. Key innovations include spatially resolved thermodynamic integration techniques and spatial block analysis for extrapolating thermodynamic properties from finite simulations. His work bridges computational chemistry, statistical mechanics, and soft matter physics, with applications in solvation thermodynamics and pressure-driven flow analysis. Publications from 2018-2019 reveal cohesive methodological advancements: extending adaptive resolution to grand canonical ensembles, refining non-equilibrium work relations, and addressing finite-size effects through integral equations. These contributions establish robust frameworks for calculating chemical potentials in dense fluids while maintaining linear momentum conservation in non-equilibrium conditions. Scientific recognition includes: Alexander von Humboldt Research Fellowship (2015) As Group Leader, he directs independent research funding and mentors junior scientists within MPI-P's collaborative environment. His work with collaborators like M. Heidari and R. Potestio demonstrates strong interdisciplinary networks in computational physics. Current projects focus on extending adaptive resolution techniques to complex molecular systems while investigating pressure-driven flows and solvation state transitions. His laboratory operates within MPI-P's polymer research infrastructure, utilizing high-performance computing resources to develop simulation tools that bridge atomistic and coarse-grained representations. The group's methodology enables precise free energy calculations previously unattainable in traditional molecular dynamics frameworks.

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Ilya Nemenmanمشاهده پروفایل

استاد

Emory UniversityUnited States

Ilya Nemenman is the Samuel Candler Dobbs Professor of Physics and Biology at Emory University's College of Arts and Sciences. He is a theoretical physicist who has been instrumental in establishing Emory as a global leader in theoretical and modeling approaches to living systems, recognized as a 2021 Simons Investigator. His educational background includes a Ph.D. from Princeton University (2000), with additional education at Belarusian State University. He completed postdoctoral training at the NEC Research Institute and the Kavli Institute for Theoretical Physics. Nemenman's research focuses on understanding how biological systems learn from and respond to their environment through what he terms "biological information processing." He seeks to identify computational primitives employed by living organisms and determine if phenomenological, coarse-grained representations of biological processes can be functionally accurate. His work spans theoretical biophysics, coarse-grained modeling in systems biology and neuroscience, information transduction in biological systems, and learning and adaptation across molecular, neural, and evolutionary scales. Nemenman leads the Theory and Modeling of Living Systems (TMLS) initiative at Emory, which unites researchers from multiple departments and institutions to understand biology with precision comparable to physical sciences. His research group studies diverse systems including primate visual brain, neural signal transduction in C. elegans, cellular suicide dynamics, and multicellular effects in cellular signaling. Simons Investigator (2021) Winship Distinguished Research Professor of Physics and Biology (2017-2020) Fellow, American Physical Society (2016) General Member, Aspen Center for Physics (2015-2025) Phi Beta Kappa mentor recognition (2013, 2015) Chair Line, Division of Biological Physics, American Physical Society (2013-2017) McDonnell Foundation 21st Century Science Initiative Fellow Nemenman mentors postdoctoral researchers, including Audrey Sederberg who joined the faculty at the University of Minnesota, and Andrew Mugler who received the NSF CAREER Award and is now an assistant professor at the University of Pittsburgh. His research has been supported by significant grants including the Simons Foundation award providing $100,000 annually for five years. He is affiliated with multiple research initiatives including The New Mexico Consortium and The Center for Nonlinear Studies at LANL, and has collaborated extensively with experimental researchers to apply theoretical approaches to real biological systems.

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