Review
Chemistry, Multidisciplinary
Ron Elber, Arman Fathizadeh, Piao Ma, Hao Wang
Summary: Time scales play a crucial role in biology, where living systems exploit variations in time scales to direct processes in desired directions. Molecular Dynamics simulations and the method of Milestoning are utilized to study dynamics of biophysical processes and enhance sampling of kinetic events, offering comprehensive pictures of complex biomolecular reactions.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2021)
Article
Chemistry, Medicinal
Lane W. Votapka, Andrew M. Stokely, Anupam A. Ojha, Rommie E. Amaro
Summary: SEEKR2 is a computational method for estimating the kinetics and thermodynamics of molecular processes. It provides equivalent or improved results compared to previous versions, with increased speed and capabilities. SEEKR2 also offers improved usability and supports simulation using OpenMM and Browndye 2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Anupam Anand Ojha, Ambuj Srivastava, Lane William Votapka, Rommie E. Amaro
Summary: Janus kinases (JAK) play a crucial role in growth, survival, and angiogenesis. The recent discovery of the V617F mutation in JAK2 leading to myeloproliferative disorders has stimulated interest in developing JAK2-specific inhibitors.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Ru Wang, Hao Wang, Wenjian Liu, Ron Elber
Summary: This study investigates the application of Milestoning in rare event kinetics calculation. Two algorithms, LPT-M and BI-M, are proposed to accurately and efficiently approximate the initial distribution of the system. The results demonstrate that both methods outperform the classical Milestoning method in terms of accuracy and computational cost.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Brajesh Narayan, Nicolae-Viorel Buchete, Ron Elber
Summary: This study used atomically detailed simulations within the Milestoning framework to investigate the molecular dissociation mechanism of Gleevec from Abl kinase. The researchers calculated the dissociation free energy profile, mean first passage time for unbinding, and explored the transition state ensemble of conformations. The study revealed that near the transition state, the highly conserved salt bridge between K217 and E286 is transiently broken.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Dhiman Ray, Sharon Emily Stone, Ioan Andricioaei
Summary: The Markovian Weighted Ensemble Milestoning (M-WEM) introduces a scheme for efficiently calculating thermodynamic and kinetic properties of biomolecular processes. It has been tested on various models and systems, demonstrating high accuracy and low computational cost, making it a potential tool for computational drug design.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Hugues Meyer, Steffen Wolf, Gerhard Stock, Tanja Schilling
Summary: A method is presented to infer the memory kernel in non-equilibrium processes, using ion dissociation in water as an example. This method improves a previously published numerical scheme and addresses the issue of truncation.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Materials Science, Multidisciplinary
E. Alarcon, L. Heller, E. de Prado, J. Kopecek
Summary: This work analyzed the effects of temperature and microstructure on the tensile behavior of superelastic NiTi wires. Cold-drawn NiTi wires with different final heat treatments were subjected to temperature gradients, and the deformation processes and microstructure changes were characterized. The results showed that the stress of localized martensitic transformation stabilized with increasing temperature, while the volume fraction of martensite decreased. Ductility exhibited a non-monotonic evolution with temperature, with higher ductility observed in samples with more microstructure recovery or recrystallization.
MATERIALS & DESIGN
(2023)
Article
Chemistry, Physical
Alfredo E. Cardenas, Allison Hunter, Hao Wang, Ron Elber
Summary: Milestoning is a theory and algorithm used to compute kinetics and thermodynamics at long time scales. It involves partitioning the phase space and running short trajectories between the boundaries of the cells to analyze the termination points and obtain kinetic and thermodynamic information. The Python script ScMiles2 is introduced as an improved version for conducting Milestoning simulations, with enhancements such as post analysis of trajectories, support for GROMACS software, automated trajectory launching, and support for complex reaction coordinates. Simulation parameters are evaluated and new algorithmic features are proposed for enhancing convergence rate of observables. Illustrations are provided for small systems and a large example.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Shriram Chennakesavalu, David J. Toomer, Grant M. Rotskoff
Summary: Coarse-grained models are essential computational tools in theoretical chemistry and biophysics, providing physical insights and efficiency compared to atomistic models. Designing effective coarse-grained models is challenging, as the mapping from fine-grained to coarse-grained configurations is not optimized. In this work, we optimize both the representation and energy function, using a graph machine learning framework.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Theodore L. Fobe, Christopher C. Walker, Garrett A. Meek, Michael R. Shirts
Summary: In this study, researchers use computational modeling techniques to address the challenges in designing non-biological foldamers. They developed CG PyRosetta, an extension to PyRosetta, which allows the folding of toy CG foldamer models. By systematically varying CG parameters in these models, they investigate different folding hypotheses and provide insights for the design process of new foldamer chemistries.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biophysics
Wenjuan Jiang, Yi-Chun Lin, Wesley Botello-Smith, Jorge E. Contreras, Andrew L. Harris, Luca Maragliano, Yun Lyna Luo
Summary: This study investigates the thermodynamics and kinetics of binding and transport of cyclic adenosine monophosphate (cAMP) through a connexin26 hemichannel. The results reveal the presence of two cAMP-binding sites, and the interplay between voltage and channel polarity on the total free energy. Additionally, the study demonstrates how cAMP dipole vector and pore diameter are influenced in a position-dependent manner.
BIOPHYSICAL JOURNAL
(2021)
Article
Polymer Science
Thao X. D. Nguyen, Tuan V. Vu, Sepideh Razavi, Dimitrios V. Papavassiliou
Summary: This work presents a methodology using dissipative particle dynamics (DPD) to simulate the flow of oil and water in a narrow slit under different flow conditions. It introduces large surfactant molecules at the oil-water interface to investigate their effects on the two-phase flow. The study provides insights into the stability of the interface under different flow conditions and verifies the accuracy of the DPD parameters.
Article
Engineering, Electrical & Electronic
Gai Yamauchi, Tadashi Ishida
Summary: A hydraulic microactuator with a coarse/fine drive-switching mechanism was developed to transport cells precisely near sensors in microfluidic devices. The microactuator achieved both coarse approach and fine adjustment of cell position on a thin film toward the microchannel wall by switching drive modes. The displacement ratio achieved using the microactuator was 13.9, with the ability to transport cyanobacteria and adjust their position near the microchannel wall with precision.
SENSORS AND ACTUATORS A-PHYSICAL
(2021)
Article
Quantum Science & Technology
Karen Hovhannisyan, Mathias R. Jorgensen, Gabriel T. Landi, Alvaro M. Alhambra, Jonatan B. Brask, Marti Perarnau-Llobet
Summary: Accurate thermometry for quantum systems is crucial for technological advancement, but practical implementations often involve coarse-grained measurements. By utilizing tools from signal processing, we can achieve good temperature estimates even with a small number of outcomes. Our findings have implications for many-body systems and nonequilibrium thermometry, providing insights into optimal coarse-grained measurements and strategies for probe-based thermometry.