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Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale…
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for…
This work presents the development, analysis and numerical simulations of a biophysical model for 3D cell deformation and movement, which couples biochemical reactions and biomechanical forces. We propose a mechanobiochemical model which…
The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
The interplay of unitary evolution and local measurements in many-body systems gives rise to a stochastic state evolution and to measurement-induced phase transitions in the pure state entanglement. In realistic settings, however, this…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…
There is a crescent use of enzymes in multiple industries and sciences, ranging from materials and fuel synthesis to pharmaceutical and food production. Their applicability in this variety of fields depends not only on their biochemical…
Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…
Dynamical symmetries are of considerable importance in elucidating the complex behaviour of strongly interacting systems with many degrees of freedom. Paradigmatic examples are cooperative phenomena as they arise in phase transitions, where…
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…
Experimental evidence shows that there is a feedback between cell shape and cell motion. How this feedback impacts the collective behavior of dense cell monolayers remains an open question. We investigate the effect of a feedback that tends…
Dynamics with choice is a generalization of discrete-time dynamics where instead of the same evolution operator at every time step there is a choice of operators to transform the current state of the system. This notion is new and…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
In this paper we study aggregation kinetics in systems of particles functionalised by complementary linkers. Most of the coarse-grained models currently employed to study large-scale self-assembly of these systems rely on effective…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…