Reply to the 'Comment on "Effects of topological constraints on linked ring polymers in solvents of varying quality"' by M. Tsige and H. Guo, , 2024, , DOI: 10.1039/D3SM01614E.

In the preceding Comment, Drs Tsige and Guo compare their findings about the -temperatures of linear chains, ring polymers and poly[]catenanes with those of previous work by us [Z. A. Dehaghani, I.

In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel.

The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g.

Electrochromic Sensor Augmented with Machine Learning for Enzyme-Free Analysis of Antioxidants.

Our study presents an electrochromic sensor that operates without the need for enzymes or multiple oxidant reagents. This sensor is augmented with machine learning algorithms, enabling the identification, classification, and prediction of six different antioxidants with high accuracy. We utilized polyaniline (PANI), Prussian blue (PB), and copper-Prussian blue analogues (Cu-PBA) at their respective oxidation states as electrochromic materials (ECMs).

Dynamics of fluid bilayer vesicles: Soft meshes and robust curvature energy discretization.

Continuum models like the Helfrich Hamiltonian are widely used to describe fluid bilayer vesicles. Here we study the molecular dynamics compatible dynamics of the vertices of two-dimensional meshes representing the bilayer, whose in-plane motion is only weakly constrained. We show (i) that Jülicher's discretization of the curvature energy offers vastly superior robustness for soft meshes compared to the commonly employed expression by Gommper and Kroll and (ii) that for sufficiently soft meshes, the typical behavior of fluid bilayer vesicles can emerge even if the mesh connectivity remains fixed throughout the simulations.

Programmable Transport of C60 by Straining Graphene Substrate.

Controlling the maneuverability of nanocars and molecular machines on the surface is essential for the targeted transportation of materials and energy at the nanoscale. Here, we evaluate the motion of fullerene, as the most popular candidate for use as a nanocar wheel, on the graphene nanoribbons with strain gradients based on molecular dynamics (MD), and theoretical approaches. The strain of the examined substrates linearly decreases by 20%, 16%, 12%, 8%, 4%, and 2%.

Counterintuitive properties of evolutionary measures: A stochastic process study in cyclic population structures with periodic environments.

Local environmental interactions are a major factor in determining the success of a new mutant in structured populations. Spatial variations in the concentration of genotype-specific resources change the fitness of competing strategies locally and thus can drastically change the outcome of evolutionary processes in unintuitive ways. The question is how such local environmental variations in network population structures change the condition for selection and fixation probability of an advantageous (or deleterious) mutant.

Nanocar swarm movement on graphene surfaces.

Investigation of nanomachine swarm motion is useful in the design of molecular transportation systems as well as in understanding the assembly process on the surface. Here, we evaluate the motion of the clusters of nanocars on graphene surfaces, using molecular dynamics (MD) simulations. The mechanism of motion of single nanocars is evaluated by considering the rotation of the wheels, direction of the nanocars' speed and comparing the characteristics of the surface motion of nanocars and similar absorbed molecules.

Electronic polarization effects on membrane translocation of anti-cancer drugs.

Free-energy calculations are crucial for investigating biomolecular interactions. However, in theoretical studies, the neglect of electronic polarization can reduce predictive capabilities, specifically for free-energy calculations. To effectively mimick polarization, we explore a (CS) model, aiming to narrow the gap between computational and experimental results.

Collective movement and thermal stability of fullerene clusters on the graphene layer.

Understanding the motion characteristics of fullerene clusters on the graphene surface is critical for designing surface manipulation systems. Toward this purpose, using the molecular dynamics method, we evaluated six clusters of fullerenes including 1, 2, 3, 5, 10, and 25 molecules on the graphene surface, in the temperature range of 25 to 500 K. First, the surface motion of clusters is studied at 200 K and lower temperatures, in which fullerenes remain as a single group.

A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions.

Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations.

Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations.

Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2.

Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides.

We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (CHOS) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (Au) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of Au/linker/tau//GaO/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide.

Monte Carlo simulation of a lattice model for the dynamics of randomly branching double-folded ring polymers.

Supercoiled DNA, crumpled interphase chromosomes, and topologically constrained ring polymers often adopt treelike, double-folded, randomly branching configurations. Here we study an elastic lattice model for tightly double-folded ring polymers, which allows for the spontaneous creation and deletion of side branches coupled to a diffusive mass transport, which is local both in space and on the connectivity graph of the tree. We use Monte Carlo simulations to study systems falling into three different universality classes: ideal double-folded rings without excluded volume interactions, self-avoiding double-folded rings, and double-folded rings in the melt state.

S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study.

SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein.

Impact of temporal correlations on high risk outbreaks of independent and cooperative SIR dynamics.

We first propose a quantitative approach to detect high risk outbreaks of independent and coinfective SIR dynamics on three empirical networks: a school, a conference and a hospital contact network. This measurement is based on the k-means clustering method and identifies proper samples for calculating the mean outbreak size and the outbreak probability. Then we systematically study the impact of different temporal correlations on high risk outbreaks over the original and differently shuffled counterparts of each network.

Locomotion of the C-based nanomachines on graphene surfaces.

We provide a comprehensive computational characterization of surface motion of two types of nanomachines with four C "wheels": a flexible chassis Nanocar and a rigid chassis Nanotruck. We study the nanocars' lateral and rotational diffusion as well as the wheels' rolling motion on two kinds of graphene substrates-flexible single-layer graphene which may form surface ripples and an ideally flat graphene monolayer. We find that the graphene surface ripples facilitate the translational diffusion of Nanocar and Nanotruck, but have little effect on their surface rotation or the rolling of their wheels.

Molecular Machinery Responsible for Graphene Oxide's Distinct Inhibitory Effects towards and Pathogens.

Graphene oxide flakes are considered as potential inhibitors for different pathogenic bacteria. However, the efficacy of inhibition changes for different types and strains of bacteria. In this work, we examine and , two common hospital-acquired infections, which react quite differently to graphene oxide flakes.

Thermal conductivity of the cell membrane in the presence of cholesterol and amyloid precursor protein.

The cell membrane is responsible for the transportation of heat between inside and outside the cell. Whether the thermal properties of the cell membrane are affected by the cholesterol concentration or the membrane proteins has not been investigated so far. Although the experimental measurement of the membrane thermal conductivity was not available until very recently, computational methods have been widely used for this purpose.

Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response.

Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it.

The hot sites of α-synuclein in amyloid fibril formation.

The role of alpha-synuclein (αS) amyloid fibrillation has been recognized in various neurological diseases including Parkinson's Disease (PD). In early stages, fibrillation occurs by the structural transition from helix to extended states in monomeric αS followed by the formation of beta-sheets. This alpha-helix to beta-sheet transition (αβT) speeds up the formation of amyloid fibrils through the formation of unstable and temporary configurations of the αS.

Effects of topological constraints on linked ring polymers in solvents of varying quality.

We investigate the effects of topological constraints in catenanes composed of interlinked ring polymers on their size in a good solvent as well as on the location of their θ-point when the solvent quality is worsened. We mainly focus on poly[n]catenanes consisting of n ring polymers each of length m interlocked in a linear fashion. Using molecular dynamics simulations, we study the scaling of the poly[n]catenane's radius of gyration in a good solvent, assuming in general that R∼mn and we find that μ = 0.

GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation.

IL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix.

Ruddlesden-Popper Phases of Methylammonium-Based Two-Dimensional Perovskites with 5-Ammonium Valeric Acid AVAMA Pb I with n = 1, 2, and 3.

5-Ammonium valeric acid (AVA) is a frequently used additive in the preparation of lead halide perovskites. However, its microscopic role as passivating, cross-linking, or templating agent is far from clear. In this work, we provide density functional theory-based structural models for the Ruddlesden-Popper (RP) phases of AVA(CHNH) Pb I for n = 1, 2, and 3 and validate with experimental data on polycrystalline samples for n = 1.