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The development of accurate constitutive models for materials that undergo path-dependent processes continues to be a complex challenge in computational solid mechanics. Challenges arise both in considering the appropriate model assumptions…
Summary: Coarse-grained normal mode analysis (NMA) is a fast computational technique to study the dynamics of biomolecules. Here we present the Najmanovich Research Group Toolkit for Elastic Networks (NRGTEN). NRGTEN is a Python toolkit…
H-bonds are known to play an important role in the folding of proteins into three-dimensional structures, which in turn determine their diverse functions. The conformations around H-bonds are important, in that they can be non-local along…
In fibrous paper materials, an exposure to a variation in moisture content causes changes in the geometrical and mechanical properties. Such changes are strongly affected by the inter-fibre bonds, which are responsible for the transfer of…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
This thesis presents the development of entropy-elastic gelatin based networks in the form of films or scaffolds. The materials have good prospects for biomedical applications, especially in the context of bone regeneration. Entropy-elastic…
While the animals' Fin-to-Limb evolution has been well-researched in biology, such morphological transformation remains under-adopted in the modern design of advanced robotic limbs. This paper investigates a novel class of overconstrained…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle…
This work addresses the optimal control of multibody systems being actuated with control forces in order to find a dynamically feasible minimum-energy trajectory of the system. The optimal control problem and its constraints are integrated…
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer protein chains…
Tissue stiffness is related to soft tissue pathologies and can be assessed through palpation or via clinical imaging systems, e.g., ultrasound or magnetic resonance imaging. Typically, the image based approaches are not suitable during…
Knowledge of the mechanical properties of materials is required for the design and analysis of engineering products, however, the characterisation of heterogeneous properties using traditional techniques is limited by spatial resolution or…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
Protein dynamics play a crucial role in many biological processes and drug interactions. However, measuring, and simulating protein dynamics is challenging and time-consuming. While machine learning holds promise in deciphering the…
Disordered spring networks are a useful paradigm to examine macroscopic mechanical properties of amorphous materials. Here, we study the elastic behavior of under-constrained spring networks, i.e.\ networks with more degrees of freedom than…
Many-body correlations in strongly coupled liquids and plasmas are critical for many applications in nanofluids, biology, and fusion-related plasma physics, but their description in fully heterogeneous environments remains challenging due…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…