Related papers: Mechanistic Modelling of Chromatin Folding to Unde…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerisation has been studied theoretically in a number of contexts, often by considering a Markov process in…
Column chromatography is an important process in downstream biopharmaceutical manufacturing that enables high-selectivity separation of proteins through various modalities, such as affinity, ion exchange, hydrophobic interactions, or a…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
A mixture of spin-1/2 fermionic atoms and molecules of paired fermionic atoms is studied in an optical lattice. The molecules are formed by an attractive nearest-neighbor interaction. A functional integral is constructed for this many-body…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…
Chromatic derivatives and series expansions of bandlimited functions have recently been introduced in signal processing and they have been shown to be useful in practical applications. We extend the notion of chromatic derivative using…
This chapter reviews the purpose and use of models from the field of complex systems and, in particular, the implications of trying to use models to understand or make decisions within complex situations, such as policy makers usually face.…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. We are developing mechanistic models for the morphogenesis of limbs, lungs, and kidneys with a view to integrate available knowledge and to…
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…
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…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…