Related papers: Energy landscape theory for cotranslational protei…
A theory of nonlinear convective depletion is set up as a nanosphere translates fast through a semidilute polymer solution. For nanospheres a self-consistent field theory in the Rouse approximation is often legitimate. A self-similar…
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…
Understanding how the effectiveness of natural photosynthetic energy harvesting systems arises from the interplay between quantum coherence and environmental noise represents a significant challenge for quantum theory. Recently it has begun…
Novel sampling algorithms can significantly impact open questions in computational biology, most notably the in silico protein folding problem. By using computational methods, protein folding aims to find the three-dimensional structure of…
Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
The construction of accurate interatomic potentials, and related fields of forces, from equilibrium conformational distributions of molecules is a crucial step in coarse-grained modeling. In this work we show that in order to develop…
We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Complex energy landscapes often arise in biological systems, e.g. for protein folding, biochemical reactions or intracellular transport processes. Their physical effects are often reflected in the first-passage times arising from these…
The ability to explain decisions made by machine learning models remains one of the most significant hurdles towards widespread adoption of AI in highly sensitive areas such as medicine, cybersecurity or autonomous driving. Great interest…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
The thesis is aimed to solve the template-free protein folding problem by tackling two important components: efficient sampling in vast conformation space, and design of knowledge-based potentials with high accuracy. We have proposed the…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
Translation is a crucial step in gene expression. During translation, macromolecules called ribosomes "read" the mRNA strand in a sequential manner and produce a corresponding protein. Translation is known to consume most of the cell's…
Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…