arXiv subjects

Ivan Saika-Voivod

Publications and source records attributed to Ivan Saika-Voivod.

At least 19 recordsLinked to original sources

arXiv2023

Probing the Viscoelastic Properties of Aqueous Protein Solutions using Molecular Dynamics Simulations

We performed molecular dynamics simulations to investigate the viscoelastic properties of aqueous protein solutions containing an antifreeze protein, a toxin protein, and bovine serum albumin. These simulations covered a temperature range from 280 K to 340 K. Our findings demonstrate that lower temperatures are associated with higher viscosity as well as a lower bulk modulus and speed of sound for all the systems studied. Furthermore, we observe an increase in the bulk modulus and speed of sound as the temperature increases up to a weak maximum while the viscosity decreases. Moreover, we analyzed the influence of protein concentration on the viscoelastic properties of the antifreeze protein solution. We observed a consistent increase in the bulk modulus, speed of sound, and viscosity as the protein concentration increased. Remarkably, our molecular dynamics simulations results closely resemble the trends observed in Brillouin scattering experiments on aqueous protein solutions. The similarity thus validates the use of simulations in studying the viscoelastic properties of protein water solutions. Ultimately, this work provides motivation for the integration of computer simulations with experimental data and holds potential for advancing our understanding of both simple and complex systems.

cond-mat.soft↗

arXiv2022

Micromagnetic simulations of clusters of nanoparticles with internal structure: Application to magnetic hyperthermia

Micromagnetic simulation results on dynamic hysteresis loops of clusters of iron oxide nanoparticles (NPs) with internal structure composed of nanorods are compared with the widely used macrospin approximation. Such calculations allowing for nanorod-composed NPs is facilitated by a previously developed coarse-graining method based on the renormalization group approach. With a focus on applications to magnetic hyperthermia, we show that magnetostatic interactions improve the heating performance of NPs in chains and triangles, and reduce heating performance in fcc arrangements. Hysteresis loops of triangular and fcc systems of complex NPs are not recovered within the macrospin approximation, especially at smaller interparticle distances. For triangular arrangements, the macrospin approximation predicts that magnetostatic interactions reduce loop area, in contrast to the complex NP case. An investigation of the local hysteresis loops of individual NPs and macrospins in clusters reveals the impact of the geometry of their neighbours on individual versus collective magnetic response, inhomogenous heating within clusters, and further differences between simulating NPs with internal structure and the use of the macrospin approximation. Capturing the internal physical and magnetic structure of NPs is thus important for some applications.

cond-mat.mtrl-sci↗

arXiv2021

Coarse-graining in micromagnetic simulations of dynamic hysteresis loops

Micromagnetic simulations based on the stochastic Landau-Lifshitz-Gilbert equation are used to calculate dynamic magnetic hysteresis loops relevant to magnetic hyperthermia. With the goal to effectively simulate room-temperature loops for large iron-oxide-based systems at relatively slow sweep rates on the order of 1 Oe/ns or less, a previously derived renormalization group approach for coarse-graining (Grinstein and Koch, Phys. Rev. Lett. 20, 207201, 2003) is modified and applied to calculating loops for a magnetite nanorod. The nanorod modelled is the building block for larger nanoparticles that were employed in preclinical studies (Dennis et al., Nanotechnology 20, 395103, 2009). The scaling algorithm is shown to produce nearly identical loops over several decades in the model grain size. Sweep-rate scaling involving the Gilbert damping parameter is also demonstrated to allow orders of magnitude speed-up of the loop calculations.

cond-mat.mtrl-sci↗

arXiv2021

Low density interior in supercooled aqueous nanodroplets expels ions to the subsurface

The interaction between water and ions within droplets plays a key role in the chemical reactivity of atmospheric and man-made aerosols. Here we report direct computational evidence that in supercooled aqueous nanodroplets a lower density core of tetrahedrally coordinated water expels the cosmotropic ions to the denser and more disordered subsurface. In contrast, at room temperature, depending on the nature of the ion the radial distribution in the droplet core is nearly uniform or elevated towards the center. We analyze the spatial distribution of a single ion in terms of a reference electrostatic model. The energy of the system in the analytical model is expressed as the sum of the electrostatic and surface energy of a deformable droplet. The model predicts that the ion is subject to a harmonic potential centered at the droplet's center of mass. We name this effect "electrostatic confinement". The model's predictions are consistent with the simulation findings for a single ion at room temperature but not at supercooling. We anticipate this study to be the starting point for investigating the structure of supercooled (electro)sprayed droplets that are used to preserve the conformations of macromolecules originating from the bulk solution.

cond-mat.soft↗

arXiv2021

Free energy surface of two-step nucleation

We test the theoretical free energy surface (FES) for two-step nucleation (TSN) proposed by Iwamatsu [J. Chem. Phys. 134, 164508 (2011)] by comparing the predictions of the theory to numerical results for the FES recently reported from Monte Carlo simulations of TSN in a simple lattice system [James, et al., J. Chem. Phys. 150, 074501 (2019)]. No adjustable parameters are used to make this comparison. That is, all the parameters of the theory are evaluated directly for the model system, yielding a predicted FES which we then compare to the FES obtained from simulations. We find that the theoretical FES successfully predicts the numerically-evaluated FES over a range of thermodynamic conditions that spans distinct regimes of behavior associated with TSN. All the qualitative features of the FES are captured by the theory and the quantitative comparison is also very good. Our results demonstrate that Iwamatsu's extension of classical nucleation theory provides an excellent framework for understanding the thermodynamics of TSN.

cond-mat.stat-mech↗

arXiv2020

Multiscale modelling of magnetostatic effects on magnetic nanoparticles with application to hyperthermia

We extend a renormalization group-based course-graining method for micromagnetic simulations to include properly scaled magnetostatic interactions. We apply the method in simulations of dynamic hysteresis loops at clinically relevant sweep rates and at 310 K of iron oxide nanoparticles (NPs) of the kind that have been used in preclinical studies of magnetic hyperthermia. The coarse-graining method, along with a time scaling involving sweep rate and Gilbert damping parameter, allow us to span length scales from the unit cell to NPs approximately 50 nm in diameter with reasonable simulation times. For both NPs and the nanorods composing them, we report effective uniaxial anisotropy strengths and saturation magnetizations, which differ from those of the bulk materials magnetite and maghemite of which they are made, on account of the combined non-trivial effects of temperature, inter-rod exchange, magnetostatic interactions and the degree of orientational order within the nanorod composites. The effective parameters allow treating the NPs as single macrospins, and we find for the test case of calculating loops for two aligned NPs that using the dipole approximation is sufficient for distances beyond 1.5 times the NP diameter. We also present a study on relating integration time step to micromagnetic cell size, finding that the optimal time step size scales approximately linearly with cell volume.

cond-mat.mes-hall↗

arXiv2019

Phase behavior of blocky charge lattice polymers: Crystals, liquids, sheets, filaments and clusters

Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and phase separation. Polymer chains containing neutral, positively charged and negatively charged monomers are placed on a cubic lattice. Only nearest neighbor interactions between charges are considered. We determine the phase diagram for a systematically varied set of sequences. We observe homogeneous fluids, liquid condensation, cluster phases, filaments, and crystal states. Of the six sequences we study, three form crystals at low temperatures. The other three sequences, which have lower charge densities, instead collapse into gel-like networks or unconnected finite clusters. Longer neutral patches along the sequence sterically limit the size and shape of low-energy structures, which is analogous to the effect of charge or limited valence in attractive colloids. Only one sequence clearly exhibits liquid behavior; this sequence has a reduced tendency to individually fold and crystallize compared to others of similar charge density and draws parallels to real IDP behavior.

cond-mat.soft↗

arXiv2019

Continuous degeneracy of the fcc kagome lattice with magnetic dipolar interactions

Results are presented on analytic and computational analyses of the spin states associated with a 3D fcc lattice composed of ABC stacked kagome planes of magnetic ions with only long-range dipole-dipole interactions. Extending previous work on the 2D kagome system, where discrete six-fold discrete degeneracy of the ground state was revealed [Holden et al. Phys. Rev. B 91, 224425 (2015)], we show that the 3D lattice exhibits a continuous degeneracy characterized by just two spherical angles involving six sublattice spin vectors. Application of a Heat Bath Monte Carlo algorithm shows that thermal fluctuations reduce this degeneracy at very low temperature in an order-by-disorder process. A magnetic field applied along directions of high symmetry also results in lifting the continuous degeneracy to a subset of states from the original set of ground states. Metropolis Monte Carlo simulation results are also presented on the temperature and system size dependence of the energy, specific heat, and magnetization, providing evidence for a phase transition at T $\simeq$ 0.38 (in units of the dipole strength). The results can be relevant to a class of magnetic compounds having the AuCu$_3$ crystal structure.

cond-mat.mtrl-sci↗

arXiv2019

Surface tension of supercooled water nanodroplets from computer simulations

We estimate the liquid-vapour surface tension from simulations of TIP4P/2005 water nanodroplets of size $N$=100 to 2880 molecules over a temperature $T$ range of 180 K to 300 K. We compute the planar surface tension $γ_p$, the curvature-dependent surface tension $γ_s$, and the Tolman length $δ$, via two approaches, one based on the pressure tensor (the "mechanical route") and the other on the Laplace pressure (the "thermodynamic route"). We find that these two routes give different results for $γ_p$, $γ_s$ and $δ$, although in all cases we find that $δ\ge 0$ and is independent of $T$. Nonetheless, the $T$ dependence of $γ_p$ is consistent between the two routes and with that of Vega and de Miguel [J. Chem. Phys. 126, 154707 (2007)] down to the crossing of the Widom line at 230 K for ambient pressure. Below 230 K, $γ_p$ rises more rapidly on cooling than predicted from behavior for $T\ge 300$ K. We show that the increase in $γ_p$ at low $T$ is correlated to the emergence of a well-structured random tetrahedral network in our nanodroplet cores, and thus that the surface tension can be used as a probe to detect behavior associated with the proposed liquid-liquid phase transition in supercooled water.

cond-mat.soft↗

arXiv2018

Phase transitions in fluctuations and their role in two-step nucleation

We consider the thermodynamic behavior of local fluctuations occurring in a stable or metastable bulk phase. For a system with three or more phases, a simple analysis based on classical nucleation theory predicts that small fluctuations always resemble the phase having the lowest surface tension with the surrounding bulk phase, regardless of the relative chemical potentials of the phases. We also identify the conditions at which a fluctuation may convert to a different phase as its size increases, referred to here as a "fluctuation phase transition" (FPT). We demonstrate these phenonena in simulations of a two dimensional lattice model by evaluating the free energy surface that describes the thermodynamic properties of a fluctuation as a function of its size and phase composition. We show that a FPT can occur in the fluctuations of either a stable or metastable bulk phase and that the transition is first-order. We also find that the FPT is bracketed by well-defined spinodals, which place limits on the size of fluctuations of distinct phases. Furthermore, when the FPT occurs in a metastable bulk phase, we show that the superposition of the FPT on the nucleation process results in two-step nucleation (TSN). We identify distinct regimes of TSN based on the nucleation pathway in the free energy surface, and correlate these regimes to the phase diagram of the bulk system. Our results clarify the origin of TSN, and elucidate a wide variety of phenomena associated with TSN, including the Ostwald step rule.

cond-mat.stat-mech↗

arXiv2018

Evaluating the Laplace pressure of water nanodroplets from simulations

We calculate the components of the microscopic pressure tensor as a function of radial distance r from the centre of a spherical water droplet, modelled using the TIP4P/2005 potential. To do so, we modify a coarse-graining method for calculating the microscopic pressure [T. Ikeshoji, B. Hafskjold, and H. Furuholt, Mol. Simul. 29, 101 (2003)] in order to apply it to a rigid molecular model of water. As test cases, we study nanodroplets ranging in size from 776 to 2880 molecules at 220 K. Beneath a surface region comprising approximately two molecular layers, the pressure tensor becomes approximately isotropic and constant with r. We find that the dependence of the pressure on droplet radius is that expected from the Young-Laplace equation, despite the small size of the droplets.

cond-mat.soft↗

arXiv2017

"Swarm relaxation": Equilibrating a large ensemble of computer simulations

It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case of this strategy, in which we run a large ensemble of $M$ independent simulations (a "swarm"), each of which is relaxed to equilibrium. We show that if $M$ is of order $10^3$, we can monitor the swarm's relaxation to equilibrium, and confirm its attainment, within $\sim 10\barτ$, where $\barτ$ is the equilibrium relaxation time. As soon as a swarm of this size attains equilibrium, the ensemble of $M$ final microstates from each run is sufficient for the evaluation of most equilibrium properties without further sampling. This approach dramatically reduces the wall-clock time required, compared to a single long simulation, by a factor of several hundred, at the cost of an increase in the total computational effort by a small factor. It is also well-suited to modern computing systems having thousands of processors, and is a viable strategy for simulation studies that need to produce high-precision results in a minimum of wall-clock time. We present results obtained by applying this approach to several test cases.

cond-mat.stat-mech↗

arXiv2015

Crystallization of Lennard-Jones nanodroplets: from near melting to deeply supercooled

We carry out molecular dynamics (MD) and Monte Carlo (MC) simulations to characterize nucleation in liquid clusters of 600 Lennard-Jones particles over a broad range of temperatures. We use the formalism of mean first-passage times to determine the rate and find that Classical Nucleation Theory (CNT) predicts the rate quite well, even when employing simple modelling of crystallite shape, chemical potential, surface tension and particle attachment rate, down to the temperature where the droplet loses metastability and crystallization proceeds through growth-limited nucleation in an unequilibrated liquid. Below this crossover temperature, the nucleation rate is still predicted when MC simulations are used to directly calculate quantities required by CNT. Discrepancy in critical embryo sizes obtained from MD and MC arises when twinned structures with five-fold symmetry provide a competing free energy pathway out of the critical region. We find that crystallization begins with hcp-fcc stacked precritical nuclei and differentiation to various end structures occurs when these embryos become critical. We confirm that using the largest embryo in the system as a reaction coordinate is useful in determining the onset of growth-limited nucleation and show that it gives the same free energy barriers as the full cluster size distribution once the proper reference state is identified. We find that the bulk melting temperature controls the rate, even though the solid-liquid coexistence temperature for the droplet is significantly lower. The value of surface tension that renders close agreement between CNT and direct rate determination is significantly lower than what is expected for the bulk system.

cond-mat.mtrl-sci↗

arXiv2015

Free energy of formation of small ice nuclei near the Widom line in simulations of supercooled water

The ST2 interaction potential has been used in a large number of simulation studies to explore the possibility of a liquid-liquid phase transition (LLPT) in supercooled water. Using umbrella sampling Monte Carlo simulations of ST2 water, we evaluate the free energy of formation of small ice nuclei in the supercooled liquid in the vicinity of the Widom line, the region above the critical temperature of the LLPT where a number of thermodynamic anomalies occur. Our results show that in this region there is a substantial free energy cost for the formation of small ice nuclei, demonstrating that the thermodynamic anomalies associated with the Widom line in ST2 water occur in a well-defined metastable liquid phase. On passing through the Widom line, we identify changes in the free energy to form small ice nuclei that illustrate how the thermodynamic anomalies associated with the LLPT may influence the ice nucleation process.

cond-mat.stat-mech↗

arXiv2014

Inverse melting in a two-dimensional off-lattice model

We carry out computer simulations of a simple, two-dimensional off-lattice model that exhibits inverse melting. The monodisperse system comprises core-softened disks interacting through a repulsive square shoulder located inside an attractive square well. By systematically varying the potential parameters, we increase the pressure range over which the liquid freezes to a crystal upon isobaric heating. The effect is largely controlled by the extent of the shoulder. Despite occurring in two dimensions, the melting transition is first order and to a liquid, rather than to a hexatic or quasicrystal phase. We also provide comment on a commonly employed correlation function used to determine the degree of translational ordering in a system.

cond-mat.mtrl-sci↗

arXiv2013

Understanding tetrahedral liquids through patchy colloids

We investigate the structural properties of a simple model for tetrahedral patchy colloids in which the patch width and the patch range can be tuned independently. For wide bond angles, a fully bonded network can be generated by standard Monte Carlo or molecular dynamics simulations of the model, providing a neat method for generating defect-free random tetrahedral networks. This offers the possibility of focusing on the role of the patch angular width on the structure of the fully bonded network. The analysis of the fully bonded configurations as a function of the bonding angle shows how the bonding angle controls the system compressibility, the strength of the pre-peak in the structure factor and ring size distribution. Comparison with models of liquid water and silica allows us to find the best mapping between these continuous potentials and the colloidal one. Building on previous studies focused on the connection between angular range and crystallization, the mapping makes it possible to shed new light on the glass-forming ability of network-forming tetrahedral liquids.

cond-mat.soft↗

arXiv2013

Heterogeneous Nucleation in the Low Barrier Regime

In simulations of the 2D Ising model, we examine heterogeneous nucleation induced by a small impurity consisting of a line of $l$ fixed spins. As $l$ increases, we identify a limit of stability beyond which the metastable phase is not defined. We evaluate the free energy barrier for nucleation of the stable phase, and show that contrary to expectation, the barrier does not vanish on approach to the limit of stability. We also demonstrate that our values for the height of the barrier yield predictions for the nucleation time (from transition state theory) and the size of the critical cluster (from the nucleation theorem) that are in excellent agreement with direct measurements, even near the limit of stability.

cond-mat.stat-mech↗

arXiv2012

Free energy surface of ST2 water near the liquid-liquid phase transition

We carry out umbrella sampling Monte Carlo simulations to evaluate the free energy surface of the ST2 model of water as a function two order parameters, the density and a bond-orientational order parameter. We approximate the long-range electrostatic interactions of the ST2 model using the reaction-field method. We focus on state points in the vicinity of the liquid-liquid critical point proposed for this model in earlier work. At temperatures below the predicted critical temperature we find two basins in the free energy surface, both of which have liquid-like bond orientational order, but differing in density. The pressure and temperature dependence of the shape of the free energy surface is consistent with the assignment of these two basins to the distinct low density and high density liquid phases previously predicted to occur in ST2 water.

cond-mat.stat-mech↗