Related papers: Molecular Dynamics Analysis of Biomolecular System…
The past two decades have witnessed tremendous progress in the microscopic description of atomic nuclei. The Topical Review `The Future of Nuclear Structure' aims at summarizing the current state-of-the-art microscopic calculations in…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…
Over the past decades, atomistic simulations of chemical, biological and materials systems have become increasingly precise and predictive thanks to the development of accurate and efficient techniques that describe the quantum mechanical…
This paper deals with the possible motion of nucleons in the nucleus, which is due to realistic inter-nucleonic forces. This approach provides new or more substantiated conclusions about the nuclear structure than those based on the…
The dynamics of a wide range of technologically important quantum systems are dominated by their interaction with just a few environmental modes. Such highly structured environments give rise to long-lived bath correlations that induce…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
Molecular Dynamics (MD) simulation is widely used to analyze the properties of molecules and materials. Most practical applications, such as comparison with experimental measurements, designing drug molecules, or optimizing materials, rely…
Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the…
This paper explores the connection between dynamical system properties and statistical physics of ensembles of such systems. Simple models are used to give novel phase transitions; particularly for finite N particle systems with many…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Molecular dynamics simulations are performed for a finite non-relativistic system of particles with Lennard-Jones potential. We study the effect of liquid-gas mixed phase on particle number fluctuations in coordinate subspace. A metastable…
Droplets are essential for spatially controlling biomolecules in cells. To work properly, cells need to control the emergence and morphology of droplets. On the one hand, driven chemical reactions can affect droplets profoundly. For…
Nuclear astrophysics is a multi-disciplinary field with a huge demand for nuclear data. Among its various fields, stellar evolution and nucleosynthesis are clearly the most closely related to nuclear physics. The need for nuclear data for…
Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A. Modern…
The extraordinary success in laser cooling, trapping, and coherent manipulation of atoms has energized the efforts in extending this exquisite control to molecules. Not only are molecules ubiquitous in nature, but the control of their…
The thermodynamic properties of nuclei are studied in a mean field model using a Skryme interaction. Properties of two component systems are investigated over the complete range of proton fraction from a system of pure neutrons to a system…