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We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…
A major challenge in molecular simulations is to describe denaturant-dependent folding of proteins order to make direct comparisons with {\it in vitro} experiments. We use the molecular transfer model, which is currently the only method…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
The Kinesin family of motor proteins are involved in a variety of cellular processes that transport materials and generate force. With recent advances in experimental techniques, such as optical tweezers which can probe individual…
We describe a general implementation of the Fynewever-Yethiraj density functional theory (DFT) for the investigation of nematic and cholesteric self-assembly in arbitrary solutions of semi-flexible polymers. The basic assumptions of the…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding…
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…
We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex ($P_1$$P_2$). The joint distribution $P(\tau_1,\tau_2)$ of unbinding lifetimes $\tau_1$ and $\tau_2$ measurable in…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
Protein Folding is concerned with the reasons and mechanism behind a protein's tertiary structure. The thermodynamic hypothesis of Anfinsen postulates an universal energy function (UEF) characterizing the tertiary structure, defined…
We explore how inherent flexibility of a protein molecule influences the mechanism controlling the kinetics of allosteric transitions using a variational model inspired from work in protein folding. The striking differences in the predicted…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component…