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Ionic microgel particles are intriguing systems in which the properties of thermo-responsive polymeric colloids are enriched by the presence of charged groups. In order to rationalize their properties and predict the behaviour of microgel suspensions, it is necessary to develop a coarse-graining strategy that starts f...
Absorption of radiation by solution is described by the solution dielectric constant and can be viewed as a specific application of the dielectric theory of solutions. For ideal solutions, the dielectric boundary value problem separates the polar response into the polarization of the void in the liquid created by the ...
We study aging in a colloidal suspension consisting of micron-sized particles in a liquid. This system is made glassy by increasing the particle concentration.
When clustering molecular dynamics (MD) trajectories into a few metastable conformational states, the Markov state models (MSMs) assumption of timescale separation between fast intrastate fluctuations and rarely occurring interstate transitions is often not valid. Hence, the naive estimation of the macrostate transiti...
We report a numerical study, covering a wide range of packing fraction $\phi$ and temperature $T$, for a system of particles interacting via a square well potential supplemented by an additional constraint on the maximum number $n_{\rm max}$ of bonded interactions. We show that when $n_{\rm max}<6$, the liquid-gas ...
Dense suspensions of particles are relevant to many applications and are a key platform for developing a fundamental physics of out-of-equilibrium systems. They present challenging flow properties, apparently turning from liquid to solid upon small changes in composition or, intriguingly, in the driving forces applied...
A stochastic field theory approach is applied to a coarse-grained polymer model that will enable studies of polymer behavior under non-equilibrium conditions. This article is focused on the validation of the new model in comparison to explicit Langevin equation simulations under conditions with analytical solutions.
The Flory chi parameter is typically assumed to depend only on the temperature, T. Experimental results often require the replacement of this chi(T) by chieff, that depends also on the monomer volume fraction, phi, chieff(phi,T). Such chieff(phi,T) can arise from two state-models, proposed for polyetheleneoxide (PEO) ...
We study conformational properties of diluted dumbbell polymers which consist of two rings that are attached to both ends of a linear spacer segment by using analytical methods of field theory and bead-spring coarse-grained molecular dynamics simulations. We investigate the influence of the relative length of the spac...
We investigate the transient bubbles that spontaneously appear in a simple liquid using molecular simulations. The objective is to deduce the free-energy of formation of the bubbles $W(s)$ from the bubble size distribution $p(s)$ through the hypothesis of a Boltzmann distribution: $W(s) = -kT \ln p(s)$.
We study a two-dimensional fluid of particles interacting through a spherically-symmetric and marginally soft two-body repulsion. This model can exist in three different crystal phases, one of them with square symmetry and the other two triangular.
In this work, we present a new model for the interpretation of the local dynamic behavior and the mechanical reinforcement mechanism in polymer nanocomposites. The temperature dependence of the dynamics in the glassy region is described by a new equation which assumes an Arrhenius component in the cooperative diffusio...
I consider the effects of polymers on the smectic phase of a host liquid crystal matrix. Focusing on the regime in which the polymers are predominately confined between the smectic layers, I find that the presence of the polymers can lead to a reentrant phase diagram with the smectic-C sandwiching the smectic-A phase ...
Composites are ideally suited to achieve desirable multifunctional effective properties since the best properties of different materials can be judiciously combined with designed microstructures. Here we establish cross-property relations for two-phase composite media that link effective elastic and electromagnetic wa...
A possibility for the observation of so-called structure resonances (SR) in electrolytes arising due to relative motion of the cluster charged nucleus and its solvation shell is demonstrated. The discussed method considers the resonant contribution of the SR to the frequency dependence of the reflection (transmission)...
Bacteriophages spreading through populations of bacteria offer relatively simple, tuneable systems for testing mathematical models of range expansion. However, such models typically assume a static state into which to expand, which is not generally valid for bacterial-bacteriophage populations, where both the host (ba...
-- A scientific hurdle in manufacturing solid films by drying colloidal layers is preventing them from fracturing. This paper examines how the drying rate of colloidal liquids influences the particle packing at the nanoscale in correlation with the crack patterns observed at the macroscale.
Brittle failure is ubiquitous in amorphous materials that are sufficiently cooled below their glass transition temperature, $T_g$. This catastrophic failure mode is limiting for amorphous materials in many applications, and many fundamental questions surrounding it remain poorly understood.
Using the bond fluctuation model we study polymer networks obtained by endlinking of symmetric 4-arm star polymers. We consider two types of systems.
A class of bistable "stator-rotor" molecules is proposed, where a stationary bridge (stator) connects the two electrodes and facilitates electron transport between them. The rotor part, which has a large dipole moment, is attached to an atom of the stator via a single sigma bond.
The underlying mechanisms and physics of catalytic Janus microswimmers is highly complex, requiring details of the associated phoretic fields and the physiochemical properties of catalyst, particle, boundaries, and the fuel used. Therefore, developing a minimal (and more general) model capable of capturing the overall...
Mathematical expressions for mass distributions around the center of gravity are derived for branched polymers with the help of the Isihara formula. We introduce the Gaussian approximation for the end-to-end vector, $\vec{r}_{G\nu_{i}}$, from the center of gravity to the $i$th mass point on the $\nu$th arm.
Directional locking occurs when a particle moving over a periodic substrate becomes constrained to travel along certain substrate symmetry directions. Such locking effects arise for colloids and superconducting vortices moving over ordered substrates when the direction of the external drive is varied.
Isolated domains in lipid monolayers exhibit shape transitions as a consequence of the competing effects of line tension and long-range dipolar interactions. Nontrivial integrals ultimately arise in instability analysis calculations of these domains.
We derive exact results for stress correlations in near-crystalline systems in two and three dimensions. We study energy minimized configurations of particles interacting through Harmonic as well as Lennard-Jones potentials, for varying degrees of microscopic disorder and quenched forces on grains.
We study the motion of an active Brownian particle (ABP) using overdamped Langevin dynamics on a two-dimensional substrate with periodic array of obstacles and in a quasi-one-dimensional corrugated channel comprised of periodically arrayed obstacles. The periodic arrangement of the obstacles enhances the persistent mo...
We demonstrate a variant of the Bond Fluctuation lattice Monte Carlo model in which moves through cis conformations are forbidden. Ring polymers in this model have a conserved quantity that amounts to a topological linking number.
The long time dynamics of the conformational transition from B-DNA to Z-DNA is shown to undergo a dynamic phase transition. We obtained the dynamic phase diagram for the stability of the front separating B and Z. The instability in this front results in two split fronts moving with different velocities.
We extend previous analysis of data for the melt-nucleus interfacial free energy, $\gamma$, gained from optical experiments on suspensions of charged colloidal spheres, which crystallize with body centred cubic (bcc) crystal structures. Compiling data from five pure species with different polydispersities and one bina...
Controlled micro- to meso-scale porosity is a common materials design goal with possible applications ranging from molecular gas adsorption to particle size selective permeability or solubility. Here, we use inverse methods of statistical mechanics to design an isotropic pair interaction that, in the absence of an ext...
We investigate the dynamics of binary mixtures of inelastic particles through event-driven molecular dynamics simulations, focusing on velocity autocorrelation functions (VACFs). The study examines two distinct particle types under varying inelasticity conditions, systematically analyzing coefficients of restitution (...
We present a study of the isotropic-nematic interface in a system of hard spherocylinders. First we compare results from Monte Carlo simulations and Onsager density functional theory for the interfacial profiles of the orientational order parameter and the density.
Here, we present the construction and calibration of a low-cost goniometer to measure contact angles by the sessile drop method. Besides, we propose a simple and fast method to calculate the uncertainty in the determination of the surface free energy (SFE) and its polar and dispersive components through the Owens-Wend...
The effects of quenched disorder on the overdamped motion of a driven particle on a periodic, asymmetric potential is studied. While for the unperturbed potential the transport is due to a regular drift, the quenched disorder induces a significant additional chaotic ``diffusive'' motion.
Nanoparticles (NPs) are widely used as drug carriers in cancer therapy due to their ability to accumulate in tumor tissue via the enhanced permeability and retention effect. However, their transport within tumors is often hindered by the dense extracellular matrix, where diffusion dominates.
We propose a simple way to perform three-dimensional (3D) rotational microrheology using two-dimensional (2D) video microscopy. The 3D rotational brownian motion of micrometric wires in a viscous fluid is deduced from their projection on the focal plane of an optical microscope objective.
We develop an analytical method for studying the properties of a non-interacting Wormlike Chain (WLC) in confined geometries. The mean field-like theory replaces the rigid constraints of confinement with average constraints, thus allowing us to develop a tractable method for treating a WLC wrapped on the surface of a ...
Using shear wave elastography, we measure the changes in the wave speed with the stress produced by a striated muscle during isometric voluntary contraction. To isolate the behaviour of an individual muscle from complementary or antagonistic actions of adjacent muscles, we select the flexor digiti minimi muscle, whose...
It is well known that viable architectural structures can be identified by locating the critical points of the gravitational potential energy congruent with some fixed surface metric. This is because, if the walls are thin, the lowest energy modes of deformation are strain-free, and thus described by surface isometrie...
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer and when bound produce a dipolar force on two neighboring monomers.
Finsler geometric surface model is studied as a coarse-grained model for membranes of three-component such as DOPC, DPPC and Cholesterol. To understand the phase separation of liquid ordered (DPPC rich) $L_o$ and the liquid disordered (DOPC rich) $L_d$, we introduce a variable $\sigma (\in \{1,-1\})$ in the triangulat...
Aqueous dispersion of Laponite at low ionic concentration is of interest since it undergoes structural evolution with respect to time, which is usually termed as ageing. In this work we study the refractive index behavior as a function of ageing time, concentration and temperature.
The shear viscosity and thermal conductivity coefficients of various liquids exhibit minima along certain trajectories on the phase diagram. These minima arise due to the crossover between the momentum and energy transport mechanisms in gas-like and liquid-like regimes.
The complexation of a polyelectrolyte with an oppositely charged spherical macroion is studied for both salt free and salty solutions. When a polyelectrolyte winds around the macroion, its turns repel each other and form an almost equidistant coil.
The order-disorder transition of a sphere-forming block copolymer thin film was numerically studied through a Cahn-Hilliard model. Simulations show that the fundamental mechanisms of pattern formation are spinodal decomposition and nucleation and growth.
Using dynamical density functional theory (DDFT) methods we investigate the laning instability of a sheared colloidal suspension. The nonequilibrium ordering at the laning transition is driven by non-affine particle motion arising from interparticle interactions.
We study the phenomenon of migration of the small molecular weight component of a binary polymer mixture to the free surface using mean field and self-consistent field theories. By proposing a free energy functional that incorporates polymer-matrix elasticity explicitly, we compute the migrant volume fraction and show...
The quartz crystal microbalance (QCM) is widely used to study surface adsorbed molecules, often of biological significance. However, the relation between raw acoustic response (frequency shift $\Delta f$ and dissipation factor $\Delta D$) and mechanical properties of the macromolecules still needs to be deciphered, pa...
We show that the time-dependent nonlinear Schrodinger equation of mean-field theory has limited utility for a one-dimensional condensate of impenetrable bosons. Mean-field theory with its associated order parameter predicts interference between split condensates that are recombined, whereas an exact many-body treatmen...
Self-folding is an emerging paradigm for the inverse design of three-dimensional structures. While most efforts have concentrated on the shape of the net, our approach introduces a new design dimension-bond specificity between the edges.
Hard spheres are arguably one of the most fundamental model systems in soft matter physics, and hence a common topic of simulation studies. Event-driven simulation methods provide an efficient method for studying the phase behavior and dynamics of hard spheres under a wide range of different conditions.
Healthy articular cartilage has excellent lubricating properties, with friction coefficients reaching extremely low values at physiological pressures. Such high-performing lubricating layer in joints is attributed to the surface hydration arising from the interplay between multiple hydrophilic biopolymers (such as hya...
It is of interest to fabricate curved surfaces in three dimensions from easily available homogeneous material in the form of flat sheets. The aim is not just to obtain a surface $M$ in $\mathbb{R}^3$ which has a desired intrinsic Riemannian metric, but to get the desired embedding $M \subset \mathbb{R}^3$ up to transl...
Colloidal systems observed in video microscopy are often analysed using the displacements correlation matrix of particle positions. In non-thermal systems, the inverse of this matrix can be interpreted as a pair-interaction potential between particles.
The self-consistent field theory (SCFT) is a powerful framework for the study of the phase behavior and structural properties of many-body systems. In particular, polymeric SCFT has been successfully applied to inhomogeneous polymeric systems such as polymer blends and block copolymer melts.
Giant unilamellar vesicles subjected to pulsed direct-current (pulsed-DC) fields are promising biomimetic systems to investigate the electroporation of cells. In strong electric fields, vesicles undergo significant deformation, which strongly alters the transmembrane potential, consequently the electroporation.
Isothermal crystallization of the mono-hydroxyl alcohol n-butanol was studied with dielectric spectroscopy in real time. The crystallization was carried out using two different sample cells at 15 temperatures between 120 K and 134 K. For all temperatures, a shift in relaxation times to shorter times was observed durin...
We study the coarsening of two-dimensional oblique stripe patterns by numerically solving potential and nonpotential anisotropic Swift-Hohenberg equations. Close to onset, all models exhibit isotropic coarsening with a single characteristic length scale growing in time as $t^{1/2}$.
The rheology of a granular shear flow is studied in a quasi-2d rotating cylinder. Measurements are carried out near the midpoint along the length of the surface flowing layer where the flow is steady and non-accelerating.
Recent studies have shown the possibility of water transport across carbon nanotubes, even in the case of nanotubes with small diameter (0.822 nm). In this case, water shows subcontinuum transport following an ordered 1D structure stabilized by hydrogen bonds.
A recent paper (Healey et al., J. Nonlin. Sci., 2013, 23:777-805.) predicted the disappearance of the stretch-induced wrinkled pattern of thin, clamped, elastic sheets by numerical simulation of the Föppl-von Kármán equations extended to the finite in-plane strain regime. It has also been revealed that for some aspect...
Magnetotactic bacteria moving on circular orbits form hydrodynamically bound states. When close to a surface and with the tilting of the field in a direction close to the perpendicular to this surface these swarms move perpendicularly to the tilting angle.
Synchronization of actively oscillating organelles such as cilia and flagella facilitates self-propulsion of cells and pumping fluid in low Reynolds number environments. To understand the key mechanism behind synchronization induced by hydrodynamic interaction, we study a model of rigid-body rotors making fixed trajec...
Ionic microgel particles in a good solvent swell to an equilibrium size determined by a balance of electrostatic and elastic forces. When crowded, ionic microgels deswell owing to a redistribution of microions inside and outside the particles.
We report on a comprehensive study of the unique adhesive properties of mats of polymethylmethacrylate (PMMA) nanofibers produced by electrospinning. Fibers are deposited on glass, varying the diameter and the relative orientation of the polymer filaments (random vs aligned configuration).
Only some special open surfaces satisfying the shape equation of lipid membranes can be compatible with the boundary conditions. As a result of this compatibility, the first integral of the shape equation should vanish for axisymmetric lipid membranes, from which two theorems of non-existence are verified:
We apply the general protocol of parameter optimization (Lee, J. et al. Phys. Chem. B 2001, 105, 7291) to the UNRES potential. In contrast to the earlier works where only the relative weights of various interaction terms were optimized, we optimize all linear parameters of the potential.
Various biological and chemical processes lead to the nucleation and growth of non-wetting fluid bubbles within the pore space of a granular medium, such as the formation of gas bubbles in liquid-saturated lake-bed sediments. In sufficiently soft porous materials, the non-wetting nature of these bubbles can result in ...
We investigate the phase behaviour of random copolymers melts via large scale Monte Carlo simulations. We observe macrophase separation into A and B--rich phases as predicted by mean field theory only for systems with a very large correlation lambda of blocks along the polymer chains, far away from the Lifshitz point....
Hydrodynamic forces may significantly affect the motion of polymers. In sheet-like cavities, such as the cell's cytoplasm and microfluidic channels, the hydrodynamic forces are long-range.
Charge correlations in dense ionic fluids give rise to novel effects such as long-range screening and colloidal stabilization which are not predicted by the classic Debye-Huckel theory. We show that a Coulomb or charge-frustrated Ising model, which accounts for both long-range Coulomb and short-range molecular interac...
Colloidal particles trapped at an interface between two fluids can form a wide range of different structures. Replacing one of the fluid with a liquid crystal increases the complexity of interactions and results in a greater range of possible structures.
Dispersions of rodlike colloidal particles exhibit a plethora of liquid crystalline states, including nematic, smectic A, smectic B, and columnar phases. This phase behavior can be explained by presuming the predominance of hard-core volume exclusion between the particles.
We have created a flat piling of disks in a numerical experiment using the Distinct Element Method (DEM) by depositing them under gravity. In the resulting pile, we then measured increments in stress and strain that were associated with a small decrease in gravity.
This paper presents the derivation of the homogenized equations that describe the macroscopic mechanical response of elastomers filled with liquid inclusions in the setting of small quasistatic deformations. The derivation is carried out for materials with periodic microstructure by means of a two-scale asymptotic ana...
Soft, amorphous solids such as tissues, foams, and emulsions are composed of deformable particles. However, the effect of single-particle deformability on the collective behavior of soft solids is still poorly understood.
We calculate the effective force between two oppositely charged and similarly charged ions fixed in water as a function of separation distance R. At short separations, R less than 1 nm, the effective force is vastly different from the $1/{\epsilon}_{s}R^2$ dependence advocated by the screened Coulomb force law (SCFL); ...
In this paper we consider thin films of AB block copolymer melts confined between two parallel plates. The plates are identical and may have a preference for one of the monomer types over the other.
On the basis of the general nonlinear theory of a hyperelastic material with initial stress, initially without consideration of the origin of the initial stress, we determine explicit expressions for the stress-dependent tensor of incremental elastic moduli. In considering three special cases of initial stress within ...
We study catalytic Janus swimmers and Escherichia coli bacteria swimming in a two-dimensional colloidal crystal. The Janus swimmers orbit individual colloids and hop between colloids stochastically, with a hopping rate that varies inversely with fuel (hydrogen peroxide) concentration.
In this work, we consider a semi-dilute solution of identical star-polymers, made of attached flexible long polymer chains of the same polymerization degree N. We first compute the effective pair-potential between star-polymers. Such a potential results from the excluded volume forces between monomers.
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the single molecule level.
When a nematic liquid crystal is confined in a porous medium with strong anchoring conditions, topological defects, called disclinations, are stably formed with numerous possible configurations. Since the energy barriers between them are large enough, the system shows multistability.
Cross-organizational collaboration in Model-Based Systems Engineering (MBSE) faces many challenges in achieving semantic alignment across independently developed system models. SysML v2 introduces enhanced structural modularity and formal semantics, offering a stronger foundation for interoperable modeling.
The quality of software produced by students is often poor. How to teach students to develop good quality software has long been a topic in computer science education and research.
Software Cost Estimation with resounding reliability,productivity and development effort is a challenging and onerous task. This has incited the software community to give much needed thrust and delve into extensive research in software effort estimation for evolving sophisticated methods.
Recently, the integration of advanced simulation technologies with artificial intelligence (AI) is revolutionizing science and engineering research. ChronoLlama introduces a novel framework that customizes the open-source LLMs, specifically for code generation, paired with PyChrono for multi-physics simulations.
Diversity and inclusion are necessary prerequisites for shaping technological innovation that benefits society as a whole. A common indicator of diversity consideration is the representation of different social groups among software engineering (SE) researchers, developers, and students.
As software projects rapidly evolve, software artifacts become more complex and defects behind get harder to identify. The emerging Transformer-based approaches, though achieving remarkable performance, struggle with long code sequences due to their self-attention mechanism, which scales quadratically with the sequenc...
Regression testing of software is a crucial but time-consuming task, especially in the context of user interface (UI) testing where multiple microservices must be validated simultaneously. Test case prioritization (TCP) is a cost-efficient solution to address this by scheduling test cases in an execution order that ma...
Natural Language Processing (NLP) is now a cornerstone of requirements automation. One compelling factor behind the growing adoption of NLP in Requirements Engineering (RE) is the prevalent use of natural language (NL) for specifying requirements in industry.
Mobile application performance is a vital factor for user experience. Yet, performance issues are notoriously difficult to detect within development environments, where their manifestations are often less conspicuous and diagnosis proves more challenging.
Recurrent neural networks (RNNs), specifically long-short term memory networks (LSTMs), can model natural language effectively. This research investigates the ability for these same LSTMs to perform next "word" prediction on the Java programming language.
Documentation is an important mechanism for disseminating software architecture knowledge. Software project teams can employ vastly different formats for documenting software architecture, from unstructured narratives to standardized documents.
Deep Learning (DL) components are routinely integrated into software systems that need to perform complex tasks such as image or natural language processing. The adequacy of the test data used to test such systems can be assessed by their ability to expose artificially injected faults (mutations) that simulate real DL...
A common application of spreadsheets is the development of models that deliver projections of the future financial statements of companies established to pursue ventures that are subject to project financing. A survey of 11 such spreadsheets prepared by a range of organisations shows that the amount of self-testing in...
A feature-oriented product line is a family of programs that share a common set of features. A feature implements a stakeholder's requirement, represents a design decision and configuration option and, when added to a program, involves the introduction of new structures, such as classes and methods, and the refine...
The amount of JavaScript embedded in Web pages has substantially grown in the past decade, leading to large and complex pages that are computationally intensive for mobile devices. In this paper, we propose JSAnalyzer, an easy-to-use tool that enables Web developers to quickly optimize and generate simpler versions of...
In this paper, we present a survey of research studies related to the cost-effectiveness of serverless approach and corresponding cost savings. We conducted a systematic literature review using Google Scholar search engine, covering the period from 2010 to 2024.
In this study, we assess the efficacy of employing the ChatGPT language model to generate solutions for coding exercises within an undergraduate Java programming course. ChatGPT, a large-scale, deep learning-driven natural language processing model, is capable of producing programming code based on textual input.

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