arXiv subjects

Robinson Cortes-Huerto

Publications and source records attributed to Robinson Cortes-Huerto.

13 recordsLinked to original sources

arXiv2026

A hidden bulk polymorph governs charge transport dimensionality in an organic semiconductor

Organic semiconductors (OSCs) are widely explored for flexible optoelectronic technologies, with performance governed not only by molecular design, but also by solid-state packing, which can give rise to polymorphism. Dinaphthothienothiophene (DNTT) is a benchmark OSC that has long been considered monomorphic. Here, we discover, isolate, and resolve the crystal structure of a previously unrecognised bulk polymorph of DNTT, termed blue DNTT owing to its characteristic blue emission. Coexisting with the well-known (green) DNTT in commercial powders, yet previously overlooked, blue DNTT represents the thermodynamically stable form. By combining X-ray diffraction, Raman, and THz spectroscopy with simulations, we demonstrate that polymorphism in DNTT reshapes the low-frequency phonon landscape and transfer-integral network, impacting charge transport. While green DNTT exhibits two-dimensional charge transport with holes more mobile than electrons, blue DNTT shows charge transport along all crystallographic directions enabled by a distinct herringbone packing. Electron mobility along the crystallographic a and b-axes in blue DNTT exceeds twice the hole mobility in the green phase. To our knowledge, this is the first reported acene-based semiconductor exhibiting three-dimensional charge transport. Polymorphism emerges as a key lever to tune charge transport dimensionality and carrier efficiency in organic semiconductors.

cond-mat.mtrl-sci↗

arXiv2026

Hidden long-range correlations in the ion distribution at the graphite / [bmim][NTf$_2$] electrified interface

A capacitor consisting of the [bmim][NTf$_2$] ionic liquid (IL) confined in between planar graphite electrodes has been investigated by molecular dynamics based on an all-atom, unpolarizable force field. Despite a few peculiarities due to the size and complexity of the ions, properties such as the density of ions throughout the capacitor, the screening of the surface charge on the electrodes by the IL and exact sum rules for the radial distribution functions of cations and anions generally comply with the results of time honored theories of the electrostatic double layer. This soothing regularity may conceal hidden correlations still compatible with the static screening rules, propagating far inside the IL the information on the state of charge of the capacitor. Evidence in this respect might have been detected by vibrational spectroscopy (see, for instance, Langmuir 2021, vol. 37, 5193-5201) showing changes in optical properties of the IL far from the charged electrodes. We show that grouping the [bmim]$^+$ and [NTf$_2$]$^-$ ions into instantaneous neutral pairs reveals an intriguing long range ordering of ions normal to the interface, driven by the capacitor state of charge. These correlations manifest themselves through the parallel orientation of the dipole moments of the neutral ion pairs. We speculate that this effect changes the average intensity of fluctuating electric fields deep in the IL, while average, static fields vanish in agreement with well established screening laws. This effect, which could change the spectroscopic properties of the IL, is present in the simulated [bmim][NTf$_2$] / graphite capacitor, but too small to be unambiguously confirmed by the present simulations with a safe margin over the error bar. The conceptual interest in these effects, however, will motivate further studies of the same or similar electrode / ionic liquid interfaces.

physics.chem-ph↗

arXiv2025

A kinetic model to simulate charge flow through an electrochemical half cell

A kinetic model of the electron transfer at the electrode / electrolyte solution interface is developed, implemented in a Monte Carlo framework, and applied to simulate this process in idealised systems consisting of the primitive model of electrolyte solutions limited by an impenetrable conducting surface. In the present implementation, a charged, spherical interface surrounding an equally spherical sample of electrolyte solution is introduced to model a single-electrode system, providing the computational analog to the conceptual half-cell picture that is widely used in electrochemistry. The electron transfer itself is described as a simple surface hopping process underlying a first order reaction corresponding to one of the coupled M/M$^+$ and X$^-$/X half reactions. Then, the electron transfer at the interface is combined with the self-diffusion of ions in the electrolyte solutions whose role is to supply reagents and disperse products, allowing the system to settle in a stationary non-equilibrium state. Simulations for the primitive model of electrolyte in contact with a charged impenetrable surface show that, after a brief transient, the samples sustain a steady current through the electrolyte solution. The results quantify the dependence of the current on: the overall charge of the electrode, the electrolyte concentration, the solvent viscosity and the kinetic parameter $k_e$ that represents the rate of the electron transfer for each ion in contact with the electrode. Since the simulated interface is very idealised, strategies to overcome the limitations of the present model are outlined and briefly discussed.

physics.chem-ph↗

arXiv2024

Density Fluctuations, Solvation Thermodynamics and Coexistence Curves in Grand Canonical Molecular Dynamics Simulations

Fluid transport across nanometric channels induced by electric, pressure and concentration gradients is ubiquitous in biological systems and fosters various applications. In this context, computer simulation setups with well-defined open-boundary equilibrium starting states are essential in understanding and assisting experimental studies. However, open-boundary computational methods are scarce and typically do not satisfy all the equilibrium conditions imposed by reality. Namely, in the absence of external gradients, 1) the system of interest (SoI) must be at thermodynamic and chemical equilibrium with an infinite reservoir of particles, 2) the fluctuations of the SoI in equilibrium should sample the grand canonical ensemble, 3) the local solvation thermodynamics, which is extremely sensitive to finite-size effects due to solvent depletion, should be correctly described. This point is particularly relevant for out-of-equilibrium systems. Finally, 4) the method should be robust enough to deal with phase transitions and coexistence conditions in the SoI. In this study, we demonstrate with prototypical liquid systems embedded into a reservoir of ideal gas particles that the adaptive resolution simulation (AdResS) method, coupled with particle insertion/deletion steps, satisfies all these requirements. Therefore, this AdResS setup is suitable for performing equilibrium and non-equilibrium simulations of open systems.

cond-mat.soft↗

arXiv2024

Smart polymer solution and thermal conductivity: How important is an exact polymer conformation?

Heat management in devices is a key to their efficiency and longevity. Here, thermal switches (TS) are of great importance because of their ability to transition between different thermal conductivity $κ$ states. While traditional TS are bulky and slow, recent experiments have suggested "smart" responsive (bio--inspired) polymers as their fast alternatives. One example is poly(N--isopropylacrylamide) (PNIPAM) in water, where $κ$ drops suddenly around a temperature $T_{\ell} \simeq 305$ K when a PNIPAM undergoes a coil--to--globule transition. At a first glance, this may suggest that the change in polymer conformation has a direct influence on TS. However, it may be presumptuous to trivially "only" link conformations with TS, especially because many complex microscopic details control macroscopic conformational transition. Motivated by this, we study TS in "smart" polymers using generic simulations. As the test cases, we investigate two different modes of polymer collapse using external stimuli, i.e., changing $T$ and cosolvent mole fraction $x_{\rm c}$. Collapse upon increasing $T$ shows a direct correlation between the conformation and $κ$ switching, while no correlation is observed in the latter case. These results suggest that the (co--)solvent--monomer interactions play a greater important role than the exact conformation in dictating TS. While some results are compared with the available experiments, possible future directions are also highlighted.

cond-mat.soft↗

arXiv2024

Tuning the thermal conductivity of silicon nanowires by surface passivation

Using large scale molecular dynamics simulations, we study the thermal conductivity of bare and surface passivated silicon nanowires (SiNWs). For the cross-sectional widths $w \le 2$ nm, SiNWs become unstable because of the surface amorphosization and also due to the evaporation of a certain fraction of Si atoms. The observed surface (in-)stability is related to a large excess energy $Δ$ of the surface Si atoms with respect to the bulk Si, resulting from the surface atoms being less coordinated and having dangling bonds.We first propose a practically relevant method that uses $Δ$ as a guiding tool to passivate these dangling bonds with hydrogen or oxygen, stabilizing the SiNWs. These passivated SiNWs are used to calculate the thermal conductivity coefficient $κ$.While the expected trend of $κ\propto w$ is observed for all SiNWs, surface passivation provides an added flexibility of tuning $κ$ with the surface coverage concentration $c$ of passivated atoms.Indeed, with respect to the bulk $κ$, passivation of SiNW reduces $κ$ by 75-80\% for $c \to 50\%$ and recovers again by 50\% for the fully passivated samples. Analyzing the phonon band structures via spectral energy density, we discuss separate contributions from the surface and the core to $κ$. Our results also reveal that surface passivation increases SiNW stiffness, contributing to the tunability in $κ$.

cond-mat.mes-hall↗

arXiv2023

Finite-size excess-entropy scaling for simple liquids

We introduce and validate a finite-size two-body excess entropy integral equation. By using analytical arguments and computer simulations of prototypical simple liquids, we show that the excess entropy $s_2$ exhibits a finite-size scaling with the inverse of the linear size of the simulation box. Since the self-diffusivity coefficient $D^*$ displays a similar finite-size effect, we show that the scaling entropy relation $D^*=A\exp(αs_2)$ also depends on the simulation box size. By extrapolating to the thermodynamic limit, we report values for the coefficients $A$ and $α$ that agree well with values available in the literature. Finally, we find a power law relation between the scaling coefficients for $D^*$ and $s_2$, suggesting a constant viscosity to entropy ratio.

cond-mat.soft↗

arXiv2022

Stabilizing $α-$helicity of polypeptide in aqueous urea: Dipole orientation or hydrogen bonding?

Urea denatures proteins due to its strong tendency to dehydrate the first solvation shell via urea-residue preferential binding. However, even after extensive experimental and computational investigations, the influence of urea on the stability of secondary structures remains elusive. For example, contrary to the common understanding, experimental studies have indicated that specific polypeptides, such as poly-alanine or alanine-rich systems, may even show an improved tendency to form secondary structures in aqueous urea. We investigate this seemingly counter-intuitive behaviour using over 15$μ$s long all-atom simulations. These results show how a delicate balance between the localized dipole orientations and hydrogen bonding dictates polypeptide solvation in aqueous urea. Our work establishes a structure-property relationship that highlights the importance of microscopic dipole-dipole orientations/interactions for the operational understanding of macroscopic protein solvation.

cond-mat.soft↗

arXiv2022

Finite-size scaling and thermodynamics of model supercooled liquids: Long-range concentration fluctuations and the role of attractive interactions

We compute partial structure factors, Kirkwood-Buff integrals (KBIs) and chemical potentials of model supercooled liquids with and without attractive interactions. We aim at investigating whether relatively small differences in the tail of the radial distribution functions result in contrasting thermodynamic properties. Our results suggest that the attractive potential favours the nucleation of long-range structures. Indeed, upon decreasing temperature, Bathia-Thornton structure factors display anomalous behaviour in the $k\to 0$ limit. KBIs extrapolated to the thermodynamic limit confirm this picture, and excess coordination numbers identify the anomaly with long-range concentration fluctuations. By contrast, the purely repulsive system remains perfectly miscible for the same temperature interval and only reveals qualitatively similar concentration fluctuations in the crystalline state. Furthermore, differences in both isothermal compressibilities and chemical potentials show that thermodynamics is not entirely governed by the short-range repulsive part of the interaction potential, emphasising the nonperturbative role of attractive interactions. Finally, at higher density, where both systems display nearly identical dynamical properties and repulsive interactions become dominant, the anomaly disappears, and both systems also exhibit similar thermodynamic properties.

cond-mat.soft↗

arXiv2021

Connecting density fluctuations and Kirkwood-Buff integrals for finite-size systems

Kirkwood-Buff integrals (KBI) connect the microscopic structure and thermodynamic properties of liquid solutions. KBI are defined in the grand canonical ensemble and evaluated assuming the thermodynamic limit (TL). In order to reconcile analytical and numerical approaches, finite-size KBI have been proposed in the literature, resulting in two strategies to obtain their TL values from computer simulations. (i) The spatial block-analysis method in which the simulation box is divided into subdomains of volume $V$ to compute fluctuations of the number of particles. (ii) A direct integration method where a corrected radial distribution function and a kernel that accounts for the geometry of the integration subvolumes are combined to obtain KBI as a function of $V$. In this work, we propose a method that connects both strategies into a single framework. We start from the definition of finite-size KBI, including the integration subdomain and an asymptotic correction to the radial distribution function, and solve them in Fourier space where periodic boundary conditions are trivially introduced. The limit $q\to 0$, equivalent to the value of the KBI in the TL, is obtained via the spatial block-analysis method. When compared to the latter, our approach gives nearly identical results for all values of $V$. Moreover, all finite-size effect contributions (ensemble, finite-integration domains and periodic boundary conditions) are easily identifiable in the calculation. This feature allows us to analyse finite-size effects independently and extrapolate the results of a single simulation to different box sizes. To validate our approach, we investigate prototypical systems, including SPC/E water and aqueous urea mixtures.

cond-mat.stat-mech↗

arXiv2020

Why Do Elastin-Like Polypeptides Possibly Have Different Solvation Behaviors in Water-Ethanol and Water-Urea Mixtures?

The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid, there are examples when a polymer collapses even in a mixture of two good solvents. This phenomenon, commonly known as co-non-solvency, is usually associated with smart polymers. Moreover, recent experiments have shown that the elastin-like polypeptides (ELPs) show co-non-solvency behavior in aqueous-ethanol mixtures. In this study, we investigate the phase behavior of ELPs in aqueous binary mixtures using molecular dynamics simulations of all-atom and complementary explicit solvent generic models. The model is parameterized by mapping the solvation free energy obtained from the all-atom simulations onto the generic interaction parameters. For this purpose, we derive segment based generic parameters for four different peptides, namely proline (P), valine (V), glycine (G) and alanine (A). Here we compare the conformational behavior of two ELP sequences, namely VPGGG and VPGVG, in aqueous-ethanol and -urea mixtures. Consistent with recent experiments, we find that ELPs show co-non-solvency in aqueous-ethanol mixtures. Ethanol molecules have preferential binding with all ELP residues and thus driving the coil-to-globule transition. On the contrary, ELP conformations show weak variation in aqueous-urea mixtures. Our simulations suggest that the glycine residues dictate the overall behavior of ELPs in aqueous-urea, where urea molecules have a rather weak preferential binding with glycine, i.e., less than kT. While the validation of the latter findings will require more detailed experimental investigation, the results presented here may provide a new twist to the present understanding of cosolvent interactions with peptides and proteins.

cond-mat.soft↗

arXiv2019

Open-Boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations

We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive resolution strategy, the system is partitioned into a domain of interest and a reservoir of non-interacting, ideal gas, particles. An external potential, applied only in the interfacial region, balances the excess chemical potential of the system. To ensure that the size of the reservoir is infinite, we introduce a particle insertion/deletion algorithm to control the density in the ideal gas region. We show that it is possible to study non-equilibrium phenomena with this open-boundary molecular dynamics method. To this aim, we consider a prototypical confined liquid under the influence of an external constant density gradient. The resulting pressure-driven flow across the atomistic system exhibits a velocity profile consistent with the corresponding solution of the Navier-Stokes equation. In contrast to available computational methods in which external forces drive the system far from equilibrium, this approach conserves momentum and closely resembles experimental conditions. The presented method can be used to study various direct and indirect out-of-equilibrium conditions in complex molecular systems.

cond-mat.stat-mech↗

arXiv2018

Spatially Resolved Thermodynamic Integration: An Efficient Method to Compute Chemical Potentials of Dense Fluids

Many popular methods for the calculation of chemical potentials rely on the insertion of test particles into the target system. In the case of liquids and liquid mixtures, this procedure increases in difficulty upon increasing density or concentration, and the use of sophisticated enhanced sampling techniques becomes inevitable. In this work we propose an alternative strategy, spatially resolved thermodynamic integration, or SPARTIAN for short. Here, molecules are described with atomistic resolution in a simulation subregion, and as ideal gas particles in a larger reservoir. All molecules are free to diffuse between subdomains adapting their resolution on the fly. To enforce a uniform density profile across the simulation box, a single-molecule external potential is computed, applied, and identified with the difference in chemical potential between the two resolutions. Since the reservoir is represented as an ideal gas bath, this difference exactly amounts to the excess chemical potential of the target system. The present approach surpasses the high density/concentration limitation of particle insertion methods because the ideal gas molecules entering the target system region spontaneously adapt to the local environment. The ideal gas representation contributes negligibly to the computational cost of the simulation, thus allowing one to make use of large reservoirs at minimal expenses. The method has been validated by computing excess chemical potentials for pure Lennard-Jones liquids and mixtures, SPC and SPC/E liquid water, and aqueous solutions of sodium chloride. The reported results well reproduce literature data for these systems.

cond-mat.soft↗