Related papers: Investigating Biological Matter with Theoretical N…
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…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
A theory of nucleus-nucleus collisions has been developed for kinetic energies substantially in excess of the binding energy. The very high pressure produced in the compound system as a result of the fusion of the two colliding nuclei is…
Here, we discuss a collection of cutting-edge techniques and applications in use today by some of the leading experts in the field of correlative approaches in single-molecule biophysics. A key difference in emphasis, compared with…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
A varying number of particles is one of the most relevant characteristics of systems of interest in nature and technology, ranging from the exchange of energy and matter with the surrounding environment to the change of particle number…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
Despite the importance of non-equilibrium statistical mechanics in modern physics and related fields, the topic is often omitted from undergraduate and core-graduate curricula. Key aspects of non-equilibrium physics, however, can be…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
The model quantum system of fermions in a one dimensional harmonic oscillator potential is investigated by a molecular dynamics method at constant temperature. Although in quantum mechanics the equipartition theorem cannot be used like in…
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…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
Molecular rotation, vibration, internal rotation, isomerization, tunneling, intermolecular dynamics of weakly and strongly interacting systems, intra-to-inter-molecular energy transfer, hindered rotation and hindered translation over…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Mathematical oncology is a rapidly evolving interdisciplinary field that uses mathematical models to enhance our understanding of cancer dynamics, including tumor growth, metastasis, and treatment response. Tumor-immune interactions play a…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…