Related papers: Optimizations of protein force fields
We advance a combined filtered/phase-field approach to topology optimization in the setting of linearized elasticity. Existence of minimizers is proved and rigorous parameter asymptotics are discussed by means of variational convergence…
Within this work, we present a novel approach to fracture simulations based on shape optimization techniques. Contrary to widely-used phase-field approaches in literature the proposed method does not require a specified 'length-scale'…
We briefly review the state-of-the-art in phase-field modeling of microstructure evolution. The focus is placed on recent applications of phase-field simulations of solid-state microstructure evolution and solidification that have been…
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…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Machine learning algorithms have been used widely in various applications and areas. To fit a machine learning model into different problems, its hyper-parameters must be tuned. Selecting the best hyper-parameter configuration for machine…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
Exact characterization of phase transitions requires sufficient configurational sampling, necessitating efficient and accurate potential energy surfaces. Molecular force fields with computational efficiency and physical interpretability are…
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…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…
We consider the optimization of the vector of grasping forces that support a known generalized force acting on the grasped object---a rigid body or a mechanism. Working in the framework of finite-dimensional normed vector spaces and their…
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…
Simulations with an explicit description of intermolecular forces using electronic structure methods are still not feasible for many systems of interest. As a result, empirical methods such as force fields (FF) have become an established…
A cost functional involving the eigenvalues of an elastic structure, that is described by a multi-phase-field equation, is optimized. This allows us to handle topology changes and multiple materials. We prove continuity and…
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…
A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…
We propose an automated protocol for designing the energy landscape of a protein energy function by optimizing its parameters. The parameters are optimized so that not only the global minimum energy conformation becomes native-like, but…
A force-based optimization method is proposed to apply the first and second kind of Piola-Kirchhoff stresses in molecular statics simulation. This method is important for finite deformation problems in which the atomistic behavior can be…