arXiv subjects

Mikko Karttunen

Publications and source records attributed to Mikko Karttunen.

At least 37 records · Page 2Linked to original sources

arXiv2021

Fine-Tuning the Polarizable CL&Pol Force Field for the Deep Eutectic Solvent Ethaline

Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019 is the first general, transferable and polarizable force field for MD simulations of different types of DESs. The original formulation contains, however, some problems that appear in simulations of ethaline and may also have a broader impact. First, the originally proposed atomic diameter parameters are unbalanced, resulting in too weak interactions between the chlorides and the hydroxyl groups of the ethylene glycol molecules. This, in turn, causes an artificial phase separation in long simulations. Second, there is an overpolarization of chlorides due to strong induced dipoles that give rise to the presence of peaks and antipeaks at very low $q$-vector values (\SI{2.4}{\per\nano\meter}) in the partial components of the structure factors. In physical terms, this is equivalent to overestimated spatial nano-scale heterogeneity. To correct these problems, we adjusted the chloride-hydroxyl radial distribution functions against \textit{ab initio} data and then extended the use of the Tang-Toennis damping function for the chlorides' induced dipoles. These adjustments correct the problems without losing the robustness of the CL\&Pol force field. The results were also compared with the non-polarizable version, the CL&P force field. We expect that the corrections will facilitate reliable use of the CL&Pol force field for other types of DESs.

cond-mat.soft↗

arXiv2021

SymPhas --General purpose software for phase-field, phase-field crystal and reaction-diffusion simulations

This work develops a new open source API and software package called \textit{SymPhas} for simulations of phase-field, phase-field crystal and reaction-diffusion models, supporting up to three dimensions and an arbitrary number of fields. \textit{SymPhas} delivers two novel program capabilities: 1) User specification of models from the associated dynamical equations in an unconstrained form and 2) extensive support for integrating user-developed discrete-grid-based numerical solvers into the API. The capability to specify general phase-field models is primarily achieved by developing a novel symbolic algebra functionality that can formulate mathematical expressions at compile time, is able to apply rules of symbolic algebra such as distribution, factoring and automatic simplification, and support user-driven expression tree manipulation. A modular design based on the CC++ template meta-programming paradigm is applied to the symbolic algebra library and general API implementation to minimize application runtime and increase the accessibility of the API for third party development. \textit{SymPhas} is written in C/CC++ and emphasizes high-performance capabilities via parallelization with OpenMP and the CC++ standard library. \textit{SymPhas} is equipped with a forward Euler solver and a semi-implicit Fourier spectral solver. Sample implementations and simulations of several phase-field models are presented, generated using the semi-implicit Fourier spectral solver.

physics.comp-ph↗

arXiv2020

Silica-Silicon Composites for Near-Infrared Reflection: A Comprehensive Computational and Experimental Study

Compact layers containing embedded semiconductor particles consolidated using pulsed electric current sintering exhibit intense, broadband near-infrared reflectance. The composites consolidated from nano- or micro-silica powder have a different porous microstructure which causes scattering at the air-matrix interface and larger reflectance primarily in the visible region. The 3 mm thick composite compacts reflect up to 72% of the incident radiation in the near-infrared region with a semiconductor microinclusion volume fraction of 1% which closely matches predictions from multiscale Monte Carlo modeling and Kubelka-Munk theory. Further, the calculated spectra predict an improvement of the reflectance by decreasing the average particle size or broadening the standard deviation. The high reflectance is achieved with minimal dissipative losses and facile manufacturing, and the composites described herein are well-suited to control the radiative transfer of heat in devices at high temperature and under harsh conditions.

physics.app-ph↗

arXiv2020

Directing Near-Infrared Photon Transport with Core@Shell Particles

Directing the propagation of near-infrared radiation is a major concern in improving the efficiency of solar cells and thermal insulators. A facile approach to scatter light in the near-infrared region without excessive heating is to embed compact layers with semiconductor particles. The directional scattering by semiconductor@oxide (core@shell) spherical particles (containing Si, InP, TiO$_2$, SiO$_2$, or ZrO$_2$) with a total radius varying from 0.1 to 4.0 μm and in an insulating medium at low volume fraction is investigated using Lorenz-Mie theory and multiscale modelling. The optical response of each layers is calculated under irradiation by the sun or a blackbody emitter at 1180 K. Reflectance efficiency factors of up to 83.7% and 63.9% are achieved for near-infrared solar and blackbody radiation in 200 μm thick compact layers with only 1% volume fraction of bare Si particles with a radius of 0.23 μm and 0.50 μm, respectively. The maximum solar and blackbody efficiency factors of layers containing InP particles was slightly less (80.2% and 60.7% for bare particles with a radius of 0.25 μm and 0.60 μm, respectively). The addition of an oxide coating modifies the surrounding dielectric environment, which improves the solar reflectance efficiency factor to over 90% provided it matches the scattering mode energies with the incident spectral density. The layers are spectrally-sensitive and can be applied as a back or front reflector for solar devices, high temperature thermal insulators, and optical filters in Gradient Heat Flux Sensors for fire safety applications.

physics.app-ph↗

arXiv2020

Jamming and force distribution in growing epithelial tissue

We investigate morphologies of proliferating cellular tissues using a newly developed numerical simulation model for mechanical cell division and migration in 2D. The model is applied to a bimodal mixture consisting of stiff cells with a low growth potential and soft cells with a high growth potential; cancer cells are typically considered to be softer than healthy cells. In an even mixture, the soft cells develop into a tissue matrix and the stiff cells into a dendrite-like network structure. When soft cells are placed inside a tissue consisting of stiff cells (to model cancer growth), the soft cells develop to a fast growing tumor-like structure that gradually evacuates the stiff cell matrix. The model also demonstrates 1) how soft cells orient themselves in the direction of the largest effective stiffness as predicted by the theory of Bischofs and Schwarz (Proc. Natl. Acad. Sci U.S.A., 100, 9274--9279 (2003) and 2) that the orientation and force generation continue a few cell rows behind the soft-stiff interface. With increasing inter-cell friction, tumor growth slows down and cell death occurs. The contact force distribution between cells is demonstrated to be highly sensitive to cell type mixtures and cell-cell interactions, which indicates that local mechanical forces can be useful as a regulator of tissue formation. The results shed new light on established experimental data.

cond-mat.soft↗

arXiv2020

Manipulation of Diatomic Molecules with 'Oriented External Electric Fields': Linear Correlations in Atomic Properties Lead to Non-Linear Molecular Responses

'Oriented external electric fields (OEEFs)' have been shown to have great potential in being able to provide unprecedented control of chemical reactions, catalysis and selectivity with applications ranging from H2 storage to molecular machines. We report a theoretical study of the atomic origins of molecular changes due to OEEFs; understanding the characteristics of OEEF-induced couplings between atomic and molecular properties is an important step toward comprehensive understanding of the effects of strong external fields on molecular structure, stability, and reactivity. We focus on the atomic and molecular (bond) properties of a set of homo- (H2, N2, O2, F2, and Cl2) and hetero-diatomic (HF, HCl, CO, and NO) molecules under intense external electric fields in the context of quantum theory of atoms in molecules (QTAIM). It is shown that atomic properties (atomic charges and energies, and localization index) correlate linearly with the field strengths, but molecular properties (bond length, electron density at bond critical point, bond length, and electron delocalization index) exhibit non-linear responses to the imposed fields. In particular, the changes in the electron density distribution alter the shapes and locations of the zero-flux surfaces, atomic volumes, atomic electron population, and localization/delocalization indices. At the molecular level, the topography and topology of the molecular electrostatic potential undergo dramatic changes. The external fields also perturb the covalent-polar-ionic characteristic of the studied chemical bonds, hallmarking the impact of electric fields on the stability and reactivity of chemical compounds. The findings are well-rationalized within the framework of the quantum theory of atoms in molecules and form a coherent conceptual understanding of these effects in prototypical molecules such as diatomics.

physics.chem-ph↗

arXiv2018

Morphology of Proliferating Epithelial Cellular Tissue

We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective division and division plane orientation. The model is applied to a bimodal mixture of stiff cells with a low growth potential and soft cells with a high growth potential. In an even mixture, the soft cells develop into a tissue matrix and the stiff cells into a dendrite-like network structure. For soft cell inclusion in a stiff cellular matrix, the soft cells develop to a fast growing tumour like structure that gradually evacuates the stiff cell matrix. With increasing inter-cell friction, the tumour growth slows down and parts of it is driven to self-inflicted cell death.

cond-mat.soft↗

arXiv2018

Improved general-purpose five-point model for water: TIP5P/2018

A new five point potential for liquid water, TIP5P/2018, is presented along with the techniques used to derive its charges from ab initio per-molecule electrostatic potentials in the liquid phase using the split charge equilibration (SQE) of Nistor et al. [J. Chem. Phys. 125, 094108 (2006)]. By taking the density and diffusion dependence on temperature as target properties, significant improvements to the behavior of isothermal compressibility were achieved along with improvements to other thermodynamic and rotational properties. While exhibiting a dipole moment close to ab initio values, TIP5P/2018 suffers from a too small quadrupole moment due to the charge assignment procedure and results in an overestimation of the dielectric constant.

cond-mat.soft↗

arXiv2018

Thermoplasmonic behavior of semiconductor nanoparticles: A comparison with metals

A number of applications in nanoplasmonics utilize noble metals, gold (Au) and silver (Ag), as the materials of choice. However, these materials suffer from problems of poor thermal and chemical stability accompanied by significant dissipative losses under high-temperature conditions. In this regard, semiconductor nanoparticles have attracted attention with their promising characteristics of highly tunable plasmonic resonances, low ohmic losses and greater thermochemical stability. Here, we investigate the size-dependent thermoplasmonic properties of semiconducting silicon and gallium arsenide nanoparticles to compare them with metallic Au nanoparticles using Mie theory. To this end, we employ experimentally estimated models of dielectric permittivity in our computations. Among the various permittivity models for Au, we further compare the Drude-Lorentz (DL) and the Drude and critical points (DCP) models. Results show a redshift in the scattering and absorption resonances for the DL model while the DCP model presents a blueshift. The dissipative damping in the semiconductor nanoparticles is strongest for the sharp electric octupole resonances followed by the quadrupole and dipole modes. However, a reverse order with strongest values for the broad dipole resonance is observed for the Au nanoparticles. A massive Drude broadening contributes strongly to the damping of resonances in Au nanoparticles at elevated temperatures. In contrast, the semiconductor nanoparticles do not exhibit any significant deterioration in their scattering and absorption resonances at high temperatures. In combination with low dissipative damping, this makes the semiconductor nanoparticles better suited for high-temperature applications in nanoplasmonics wherein the noble metals suffer from excessive heating.

cond-mat.mes-hall↗

arXiv2017

Molecular Dynamics Study of Conformations of Beta-Cyclodextrin and its Eight Derivatives in Four Different Solvents

Understanding the atomic level interactions and the resulting structural characteristics is required for developing beta-cyclodextrin ($β$CD) derivatives for pharmaceutical and other applications. The effect of four different solvents on the structures of the native $β$CD and its hydrophilic (methylated $β$CD; ME$β$CD and hydroxypropyl $β$CD; HP$β$CD) and hydrophobic derivatives (ethylated $β$CD; ET$β$CD) were explored using molecular dynamics (MD) simulations and solvation free energy calculations. The native $β$CD, 2-ME$β$CD, 6-ME$β$CD, 2,6-DM$β$CD, 2,3,6-TM$β$CD, 6-HP$β$CD, 2,6-HP$β$CD and 2,6-ET$β$CD in non-polar solvents (cyclohexane; CHX and octane; OCT) were stably formed in symmetric cyclic cavity shape through their intramolecular hydrogen bonds. In contrast, $β$CDs in polar solvents (methanol; MeOH and water; WAT) exhibited large structural changes and fluctuations leading to significant deformations of their cavities. Hydrogen bonding with polar solvents was found to be one of the major contributors to this behavior: solvent-\b{eta}CD hydrogen bonding strongly competes with intramolecular bonding leading to significant changes in structural stability of $β$CDs. The exception to this is the hydrophobic 2,6-ET$β$CD which retained its spherical cavity in all solvents. Based on this, it is proposed that 2,6-ET$β$CD can act as a sustained release drug carrier.

cond-mat.soft↗

arXiv2017

Non-conformal coarse-grained potentials for water

Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called Approximate Non-Conformal (ANC) and generalized Stockmayer potentials as the starting points. They are fitted using the radial density function and the density of the atomistic SPC/E model by downhill simplex optimization. We compare the results with monatomic water (mW), ELBA, as well as with direct Iterative Boltzmann Inversion (IBI) of SPC/E. The results show that symmetrical potentials result in non-transferable models, that is, they need to be reparametrized for new state-points. This indicates that transferability may require more complex models. Furthermore, the results also show that the addition of a point dipole is not sufficient to make the potentials accurate and transferable to different temperatures (300 K-500 K) and pressures without an appropriate choice of properties as targets during model optimization.

cond-mat.soft↗

arXiv2017

Propulsion and controlled steering of magnetic nanohelices

Externally controlled motion of micro and nanomotors in a fluid environment constitutes a promising tool in biosensing, targeted delivery and environmental remediation. In particular, recent experiments have demonstrated that fuel-free propulsion can be achieved through the application of external magnetic fields on magnetic helically shaped structures. The magnetic interaction between helices and the rotating field induces a torque that rotates and propels them via the coupled rotational-translational motion. Recent works have shown that there exist certain optimal geometries of helical shapes for propulsion. However, experiments show that controlled motion remains a challenge at the nanoscale due to Brownian motion that interferes with the deterministic motion and makes it difficult to achieve controlled steering. In the present work we employ quantitatively accurate simulation methodology to design a setup for which magnetic nanohelices of 30 nm in radius, with and without cargo, can be accurately propelled and steered in the presence of thermal fluctuations. In particular, we demonstrate fast transport of such nanomotors and devise protocols in manipulating external fields to achieve directionally controlled steering at biologically relevant temperatures.

physics.flu-dyn↗

arXiv2017

Controlled propulsion and separation of helical particles at the nanoscale

Controlling the motion of nano and microscale objects in a fluid environment is a key factor in designing optimized tiny machines that perform mechanical tasks such as transport of drugs or genetic material in cells, fluid mixing to accelerate chemical reactions, and cargo transport in microfluidic chips. Directed motion is made possible by the coupled translational and rotational motion of asymmetric particles. A current challenge in achieving directed and controlled motion at the nanoscale lies in overcoming random Brownian motion due to thermal fluctuations in the fluid. We use a hybrid lattice-Boltzmann Molecular Dynamics method with full hydrodynamic interactions and thermal fluctuations to demonstrate that controlled propulsion of individual nanohelices in an aqueous environment is possible. We optimize the propulsion velocity and the efficiency of externally driven nanohelices. We quantify the importance of the thermal effects on the directed motion by calculating the Péclet number for various shapes, number of turns and pitch lengths of the helices. Consistent with the experimental microscale separation of chiral objects, our results indicate that in the presence of thermal fluctuations at Péclet numbers $>10$, chiral particles follow the direction of propagation according to its handedness and the direction of the applied torque making separation of chiral particles possible at the nanoscale. Our results provide criteria for the design and control of helical machines at the nanoscale.

physics.flu-dyn↗

arXiv2016

Molecular Dynamics simulations and Kelvin Probe Force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures

The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations qualitatively match the experimental results, with 100s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.

cond-mat.soft↗

arXiv2016

Alpha-tocopherol inhibits pore formation in the oxidized bilayers

In biological membranes, alpha-tocopherols (α-toc; vitamin E) protect polyunsaturated lipids from free radicals. Although the interactions of α-toc with non-oxidized lipid bilayers have been studied, their on oxidized bilayers remain unknown. In this study, atomistic molecular dynamics (MD) simulations of oxidized lipid bilayers were performed with varying concentrations of α-toc. Bilayers with 1-palmitoyl-2-lauroyl-sn-glycero-3-phosphocholine (PLPC) lipids and its aldehyde derivatives at 1:1 ratio were studied. Our simulations show that oxidized lipids self-assemble into aggregates with a water pore rapidly developing across the lipid bilayer. The free energy of transporting an α-toc molecule in a lipid bilayer suggests that α-tocs can passively adsorb into the bilayer. When α-toc molecules were present at low concentrations in bilayers containing oxidized lipids, the formation of water pores was slowed down. At high α-toc concentra-tions, no pores were observed. Based on the simulations, we propose that the mechanism of how α-toc inhibits pore formation in bilayers with oxidized lipids is the follow-ing: α-tocs trap the polar groups of the oxidized lipids at the membrane-water interface resulting in a decreased probability for the oxidized lipids to reach contact with the two leaflets and initiate pore formation. This demon-strates that α-toc molecules not only protect the bilayer from oxidation but also help to stabilize the bilayer after lipid peroxidation occurs. These results will help in de-signing more efficient molecules to protect membranes from oxidative stress.

physics.bio-ph↗

arXiv2016

Getting excited: Challenges in quantum-classical studies of excitons in polymeric systems

A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) was performed to describe conformational properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE). DFT calculations were employed to improve and develop force field parameters for MM/MD simulations. Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation were utilized to describe excited states of the systems. Reliability of the excitation energies based on the MM/MD conformations was examined and compared to the excitation energies from DFT conformations. The results show an overall agreement between the optical excitations based on MM/MD conformations and DFT conformations. This allows for calculation of excitation energies based on MM/MD conformations.

cond-mat.mes-hall↗

arXiv2016

Solvent effects on optical excitations of poly para phenylene ethynylene studied by QM/MM simulations based on Many-Body Green's Functions Theory

Electronic excitations in dilute solutions of poly para phenylene ethynylene (poly-PPE) are studied using a QM/MM approach combining many-body Green's functions theory within the $GW$ approximation and the Bethe-Salpeter equation with polarizable force field models. Oligomers up to a length of 7.5\,nm (10 repeat units) functionalized with nonyl side chains are solvated in toluene and water, respectively. After equilibration using atomistic molecular dynamics (MD), the system is partitioned into a quantum region (backbone) embedded into a classical (side chains and solvent) environment. Optical absorption properties are calculated solving the coupled QM/MM system self-consistently and special attention is paid to the effects of solvents. The model allows to differentiate the influence of oligomer conformation induced by the solvation from electronic effects related to local electric fields and polarization. It is found that the electronic environment contributions are negligible compared to the conformational dynamics of the conjugated PPE. An analysis of the electron-hole wave function reveals a sensitivity of energy and localization characteristics of the excited states to bends in the global conformation of the oligomer rather than to the relative of phenyl rings along the backbone.

cond-mat.mtrl-sci↗

arXiv2016

The good, the bad and the user in soft matter simulations

Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues.

cond-mat.soft↗