Related papers: Mechanistic Modelling of Chromatin Folding to Unde…

We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…

Virtually all aspects of many-body atomic physics are challenging: experiments are technically demanding, datasets have become enormous, and the memory and CPU requirements for classical simulation of generic quantum systems often scale…

Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…

Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…

Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…

Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…

Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…

Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…

Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…

The combination of theory and simulation is necessary in the investigation of properties of complex systems where each method alone cannot do the task properly. Theory needs simulation to test ideas and to check approximations. Simulation…

Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…

The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…

Materials with thickness ranging from a few nanometers to a single atomic layer present unprecedented opportunities to investigate new phases of matter constrained to the two-dimensional plane.Particle-particle Coulomb interaction is…

Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…

Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…

We regard explanations as a blending of the input sample and the model's output and offer a few definitions that capture various desired properties of the function that generates these explanations. We study the links between these…

Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…

Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off…

Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based…