Related papers: Variational Scheme to Compute Protein Reaction Pat…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
Adaptive precision molecular dynamics simulations have developed along energy- and force-coupling approaches, which allow for a continuous transition between different particle descriptions or interaction potentials. Most approaches…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Accurate simulations of molecules require high-level electronic-structure theory in combination with rigorous methods for approximating the quantum dynamics. Machine-learning approaches can significantly reduce the computational expense of…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…
Biomolecular thermodynamics and spectroscopy depend on relative conformer energies, local curvatures, and collective dipole fluctuations on the potential-energy surface. Conventional molecular mechanics force fields enable large-scale…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
Applying electric fields is an attractive way to control and manipulate single particles or molecules, e.g., in lab-on-a-chip devices. However, the response of nanosize objects in electrolyte solution to external fields is far from trivial.…
Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…