Related papers: Enumerating Designing Sequences in the HP Model
Voids exist in proteins as packing defects and are often associated with protein functions. We study the statistical geometry of voids in two-dimensional lattice chain polymers. We define voids as topological features and develop a simple…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
We investigate the time evolution of the heteropolymer model introduced by Iori, Marinari and Parisi to describe some of the features of protein folding mechanisms. We study how the (folded) shape of the chain evolves in time. We find that…
Packing problems, which ask how to arrange a collection of objects in space to meet certain criteria, are important in a great many physical and biological systems, where geometrical arrangements at small scales control behaviour at larger…
This work considers the behavior of the height distributions of the equipotential lines in a region confined by two interfaces: a cathode with an irregular interface and a distant flat anode. Both boundaries, which are maintained at…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
Topological and metric entropies of the DNA sequences from different organisms were calculated. Obtained results were compared each other and with ones of corresponding artificial sequences. For all envisaged DNA sequences there is a…
Protein sequence generation via stochastic attention produces plausible family members from small alignments without training, but treats all stored sequences equally and cannot direct generation toward a functional subset of interest. We…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly, and is highly relevant in material design and biology. Here, we show that specific, but promiscuous, short-range binding interactions make…
We used a coarse-grained model to study the geometric and dynamic properties of flexible entangled polymer chains dissolved in explicit athermal solvents. Our simulations successfully reproduced the geometrical properties including the…
We use an off-lattice microscopic model for solutions of equilibrium polymers (EP) in a lamellar shear flow generated by means of a self-consistent external field between parallel hard walls. The individual conformations of the chains are…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design…
Non-proportional hazards (NPH) are often observed in clinical trials with time-to-event endpoints. A common example is a long-term clinical trial with a delayed treatment effect in immunotherapy for cancer. When designing clinical trials…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We study a model of "elastic" lattice polymer in which a fixed number of monomers $m$ is hosted by a self-avoiding walk with fluctuating length $l$. We show that the stored length density $\rho_m = 1 - <l>/m$ scales asymptotically for large…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…