Related papers: Nonlinear backbone torsional pair correlations in …
Backpropagation (BP) has been pivotal in advancing machine learning and remains essential in computational applications and comparative studies of biological and artificial neural networks. Despite its widespread use, the implementation of…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
Nonlinear effects in protein dynamics are expected to play role in function, particularly of allosteric nature, by facilitating energy transfer between vibrational modes. A recently proposed method focusing on the non-Gaussian shape of the…
From protein motifs to black holes, topological solitons are pervasive nonlinear excitations that are robust and can be driven by external fields. So far, existing driving mechanisms all accelerate solitons and antisolitons in opposite…
Motor-proteins are responsible for transport inside cells. Harnessing their activity is key towards developing new nano-technologies, or functional biomaterials. Cytoskeleton-like networks, recently tailored in vitro, result from the…
Understanding the temporal properties of longitudinal data is critical for identifying trends, predicting future events, and making informed decisions in any field where temporal data is analysed, including health and epidemiology, finance,…
We analyse the dynamics of overlapping antiparallel treadmilling microtubules in the presence of crosslinking processive motor proteins that counterbalance an external force. We show that coupling the force-dependent velocity of motors and…
We study non-interacting Poissonian run-and-tumble particles (RTPs) in two dimensions whose velocity orientations are controlled by an arbitrary circular distribution $Q(\phi)$. RTP-type active transport has been reported to undergo…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
Bartussek, Hanggi and Kissner studied a rocking ratchet system, in which a Brownian particle is subject to an asymmetric periodic potential together with an oscillating force, and found that the direction of the macroscopic current can be…
Environments with immobile obstacles or void regions that inhibit and alter the motion of individuals within that environment are ubiquitous. Correlation in the location of individuals within such environments arises as a combination of the…
The fishbone-induced transport of alpha particles is computed for the ITER 15 MA baseline scenario, using the nonlinear hybrid Kinetic-MHD code XTOR-K. Two limit cases have been studied, in order to analyse the characteristic regimes of the…
Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO$_3^-$) group, is the most studied form of protein…
Non-Hermitian quasicrystal constitutes a unique class of disordered open system with PT-symmetry breaking, localization and topological triple phase transitions. In this work, we uncover the effect of quantum correlation on phase…
Non-communicable disease is the leading cause of death, emphasizing the need for accurate prediction of disease progression and informed clinical decision-making. Machine learning (ML) models have shown promise in this domain by capturing…
The transport of ligands, such as NO or O$_2$, through internal cavities is essential for the function of globular proteins, including hemoglobin, myoglobin (Mb), neuroglobin, truncated hemoglobins, or cytoglobin. For Mb, several internal…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
Recent experimental findings on a protein showed the diffusion of vibrational energy does not occur along the backbone interaction,as it might be expected, but prevalently on non-bonded contacts. These results are explained presenting a…