Article
Chemistry, Analytical
Bing Xu, Yang Shi, Deng Pan, Dong Wu
Summary: Microfluidic one-way particle transport is a newly emerging field. This study proposes a novel design of 3D microstructures, named one-way particle diode, which allows particle transport in one direction and has potential applications in various research areas.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Optics
G. A. Dominguez-Castro, R. Paredes
Summary: We report a robust delocalization transition of a pair of hard-core bosons moving in a one-dimensional quasicrystal with power-law hopping, where quasiperiodicity suppresses transport in the regime of strong interactions before enhancing it when the quasiperiodic modulation is increased. By introducing an effective Hamiltonian for strong interactions, we uncover the mechanism behind the delocalization transition. Stationary single-particle properties and two-particle correlations confirm our findings.
Editorial Material
Nanoscience & Nanotechnology
Nadim Darwish
Summary: Transport measurements through a single molecule reveal the mechanism of the catalytic Suzuki-Miyaura cross-coupling reaction.
NATURE NANOTECHNOLOGY
(2021)
Article
Physics, Multidisciplinary
Nicholas Zobrist, W. Hawkins Clay, Gregoire Coiffard, Miguel Daal, Noah Swimmer, Peter Day, Benjamin A. Mazin
Summary: This study explores a method to improve the resolving power of nonmembrane MKIDs through a simple bilayer design. The results show that, without increasing the fabrication complexity, the resolving power can be roughly doubled, with the main reason being the inability of high energy phonons to enter the additional layer.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Physical
Guodong Hu, Yonghong Zhang, Zhiping Yu, Tiejun Cui, Wanling Cui
Summary: This research used molecular dynamics simulations to reveal the binding mechanism of the preQ(1) riboswitch aptamer with preQ1 ligands. By decomposing the binding free energy, specific nucleotides and ions were found to play crucial roles in the binding process. The study also revealed two pathways for ligand dissociation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
S. K. Adhikari
Summary: The study focuses on the formation of spin-1 symbiotic spinor solitons in a hyperfine spin F = 1 ferromagnetic Bose-Einstein condensate, showing that quasi-1D and quasi-2D solitons exhibit different spatial density structures.
Article
Materials Science, Biomaterials
Marco E. Miali, Wei Chien, Thomas Lee Moore, Alessia Felici, Anna Lisa Palange, Michele Oneto, Dmitry Fedosov, Paolo Decuzzi
Summary: A microfluidic chip is designed and validated as a platform to assess the mechanical behavior of fluid-borne particles. The behavior of particles with different geometries and mechanical attributes under flow conditions is investigated through experimental and computational methods.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Chemistry, Physical
Alexey A. Gavrilov, Elena Yu. Kramarenko
Summary: This study investigates the total conservative force acting on two charges in a polar liquid using dissipative particle dynamics and coarse-grained molecular dynamics simulations, showing that this force obeys Coulomb's law at large distances between the charges. The dielectric response of a polar liquid can be decomposed into two contributions: the reorientation of the dipoles and the density redistribution.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Review
Engineering, Electrical & Electronic
Peng Su, Chunhui Ren, Yusheng Fu, Jinhong Guo, Jiuchuan Guo, Qi Yuan
Summary: Microfluidic technology has great application potential in various fields, and magnetophoresis is an effective method to manipulate particles in liquid media using magnetic field force. Understanding the key components and parameters of magnetophoresis equipment can provide a simple, efficient, and cost-effective solution for bioparticle analysis.
SENSORS AND ACTUATORS A-PHYSICAL
(2021)
Review
Biochemical Research Methods
Francesco Del Giudice, Gaetano D'Avino, Pier Luca Maffettone
Summary: Microfluidic devices can precisely manipulate droplets and particles, enabling the fabrication of crystal-like structures formed by hydrodynamic interactions among droplets or particles.
Article
Materials Science, Multidisciplinary
Ziyi Feng, Boyu Zhou, Xin Su, Ting Wang, Shu Guo, Huazhe Yang, Xiaoting Sun
Summary: This study aimed to develop a multiphasic Janus particle system for programmed drug delivery. Triple-phase Janus microparticles with different degradation properties in each phase were generated using a one-step microfluidic preparation process. The particles exhibited programmed degradation behaviors and partial degradation as well as triggered cargo release in response to changes in temperature or pH. By modifying the particles with graphene nanosheets and silica nano-spheres, their functions were enriched. Co-loading of doxorubicin and curcumin in the triple-phase microparticles enabled zonal drug loading, and the particles showed programmed release behavior and enhanced tumor inhibition efficacy.
MATERIALS & DESIGN
(2023)
Review
Biophysics
Liyuan Gong, Andrew Cretella, Yang Lin
Summary: Microfluidic technology offers a promising tool for various applications and provides advantages such as contactless operation, label-free detection, high accuracy, good sensitivity, and minimal reagent requirements. However, the release and recovery efficiency of trapped particles have often been overlooked. This review highlights the importance of both capture and release mechanisms in microfluidic systems and assesses their effectiveness.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Mathematics, Applied
Przemyslaw Gawronski, Alfio Borzi, Krzysztof Kulakowski
Summary: This study investigates the system of two resources and one consumer within the Rosenzweig-MacArthur model, with a Holling type II functional response. The results show that oscillations of C and mutually synchronized R-i are destabilized when consumption rates are modified, leading the system towards fixed points or limit cycles with smaller amplitudes. The consumer is unable to change the preferred resource due to the symmetry between the resources.
Article
Chemistry, Multidisciplinary
Xuexia Lin, Jianlong Su, Shufeng Zhou
Summary: The concentration gradient and fluid shear stress in the cell microenvironment were investigated using microfluidic technology. The microfluidic chip was designed using the Darcy-Weisbach equation and computational fluid dynamics modeling, and the distribution of fluid shear stress on the cell model with different micro-channels was studied. The diffusion-convection equation and incompressible laminar flow model were used to simulate the concentration gradient profiles. The experimental data showed agreement with the model simulations, and the method was applied to study single cells, tumor development, and therapeutic applications.
CHINESE CHEMICAL LETTERS
(2022)
Article
Chemistry, Physical
Schuyler P. Lockwood, Ricardo B. Metz
Summary: The bond strength and photodissociation dynamics of MgI+ are studied using theory, photodissociation spectroscopy, and photofragment velocity map imaging. The photodissociation spectrum of MgI+ shows a broad and unstructured profile from 17,000 to 21,500 cm(-1), with perpendicular anisotropy observed in the photofragment images. Bond dissociation energy is determined to be 203.0 +/- 1.8 kJ/mol (2.10 +/- 0.02 eV) at 17,000 +/- 150 cm(-1). Resonance enhanced two-photon dissociation is observed at photon energies of 33,000-41,000 cm(-1), leading to the formation of exclusively I+ fragments.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Zheyong Fan, Yanzhou Wang, Penghua Ying, Keke Song, Junjie Wang, Yong Wang, Zezhu Zeng, Ke Xu, Eric Lindgren, J. Magnus Rahm, Alexander J. Gabourie, Jiahui Liu, Haikuan Dong, Jianyang Wu, Yue Chen, Zheng Zhong, Jian Sun, Paul Erhart, Yanjing Su, Tapio Ala-Nissila
Summary: We present the latest advancements in machine-learned potentials based on the neuroevolution potential framework and their implementation in the open-source package GPUMD. The accuracy of the models is improved by enhancing the radial and angular descriptors, and their efficient implementation in graphics processing units is described. Comparisons with state-of-the-art MLPs demonstrate the superior accuracy and computational efficiency of the NEP approach. Additionally, an active-learning scheme based on the latent space of a pre-trained NEP model is proposed, and three Python packages are introduced for integrating GPUMD into Python workflows.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Navid Afrasiabian, Venkat Balasubramanian, Colin Denniston
Summary: By employing molecular dynamics simulations, this study focuses on the dispersion and orientation of nanorods in an unentangled polymer melt, with a particular emphasis on the effect of nanorod concentration. The results indicate that the concentration of rods directly affects the phase behavior of the system, with the formation of nematic clusters at lower concentrations and more isotropic and less structured rod configurations at higher concentrations. The polymer chains near the rod surface exhibit extension along the direction of the rods. The dispersion and orientation of the nanorods can be attributed to the competing forces of depletion entropic forces driving the formation of rod clusters, enthalpic effects promoting rod-polymer mixing, and entropic losses associated with polymer interpenetration in the rod clusters.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Vaibhav Thakore, Tapio Ala-Nissila, Mikko Karttunen
Summary: This study investigates the temperature and polarization-dependent optical anisotropy of metallic and semiconductor nanowires, showing differences in scattering and absorption efficiencies under different conditions.
SCIENTIFIC REPORTS
(2022)
Article
Thermodynamics
Penghua Ying, Ting Liang, Ke Xu, Jianbin Xu, Zheyong Fan, Tapio Ala-Nissila, Zheng Zhong
Summary: In this paper, an efficient machine-learned neuroevolution potential model is developed to study the thermal transport in three allotropes of phosphorus. The thermal conductivity values of these allotropes are predicted using molecular dynamics simulations, and the underlying reasons for their significantly different thermal conductivity values are revealed through spectral decomposition, phonon eigenmodes, and phonon participation ratio.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2023)
Article
Physics, Multidisciplinary
Hossein Vahid, Alberto Scacchi, Maria Sammalkorpi, Tapio Ala-Nissila
Summary: Multivalent ions in polyelectrolyte solutions cause electrostatic correlations that can alter ion distributions and interactions. Our simulations demonstrate that ion shape and concentration, in addition to valency, can control rigid like-charged polyelectrolyte interactions. We show a correlation between the orientation of aspherical ions and the induced polyelectrolyte attraction through multivalency. This external control over interaction type, strength, and range can guide the self-assembly of like-charged polyelectrolytes.
PHYSICAL REVIEW LETTERS
(2023)
Article
Materials Science, Multidisciplinary
K. R. Elder, Zhi-Feng Huang, Tapio Ala-Nissila
Summary: This paper presents a systematic examination of graphene/hexagonal boron nitride (g/hBN) bilayers using a recently developed two-dimensional phase field crystal model that considers out-of-plane deformations. The system parameters are determined by matching the stacking energies and heights of g/hBN bilayers to those obtained from quantum-mechanical density functional theory calculations. The study reveals that out-of-plane deformations reduce the energies of inversion domain boundaries in hBN, and the coupling between graphene and hBN layers results in a bilayer defect configuration consisting of an inversion boundary in hBN and a domain wall in graphene. Simulations of twisted bilayers demonstrate the structure, energy, and elastic properties of moire patterns, and show a transition from well-defined hexagonal network of domain boundaries and junctions to smeared-out patterns as the misorientation angle between the layers increases.
PHYSICAL REVIEW MATERIALS
(2023)
Article
Transportation
Sara Heydari, Zhiren Huang, Takayuki Hiraoka, Alejandro Ponce de Leon Chavez, Tapio Ala-Nissila, Lasse Leskela, Mikko Kivela, Jari Saramaki
Summary: This study investigates the use of multiple data sources, including mobile phones, road traffic sensors, and companies like Google and Facebook, to model mobility patterns and estimate mobility flows in Finland before and during the disruption caused by the COVID-19 pandemic in early 2020. The results show that the model combining past baseline from mobile phone data with up-to-date road traffic data achieves the highest accuracy, followed by radiation and gravity models augmented with traffic data. The findings highlight the usefulness of publicly available road traffic data in mobility modeling and pave the way for a data fusion approach to estimating mobility flows.
TRAVEL BEHAVIOUR AND SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Navid Afrasiabian, Matthew Wei, Colin Denniston
Summary: Solid-state nanopore sensors are a promising solution for the rising demand for genome sequencing. Single-molecule sensing technologies require single-file translocation for accurate detection, and a previous study discovered a pulley effect in a pressure-driven translocation system. In this study, the pulley effect is further investigated in the presence of pressure-driven fluid flow and an opposing force from an electrostatic field to increase single-file capture probability.
Article
Physics, Multidisciplinary
Hamidreza Khalilian, Jalal Sarabadani, Tapio Ala-Nissila
Summary: Using Langevin dynamics simulations, we found that the presence of active rods in the environment facilitates the translocation of a flexible linear polymer through a nanopore, even when there are initially more monomers on the cis side. Structural analysis revealed that successful translocation events result in a folded structure of the trans-side subchain induced by the active rods. By varying the rod number density and keeping the initial number of monomers on the cis side subchain fixed, we mapped out a state diagram for successful translocation events, showing a competition between facilitation and crowding.
PHYSICAL REVIEW RESEARCH
(2023)
Article
Physics, Fluids & Plasmas
Xiang Yang, Sahin Buyukdagli, Alberto Scacchi, Maria Sammalkorpi, Tapio Ala-Nissila
Summary: EP mobility reversal refers to the phenomenon where the direction of polymer drift driven by an external electric field is reversed due to the change in sign of the counterion-dressed surface charge. In order to understand this counterintuitive effect, a strong-coupling-dressed Poisson-Boltzmann approach is applied to the cylindrical geometry of the polyelectrolyte-salt system. The derived analytical polymer mobility formula predicts that the increment of monovalent salt, the decrease of multivalent counterion valency, and the increase of the dielectric permittivity of the solvent suppress charge correlations and increase the concentration of multivalent bulk counterions required for EP mobility reversal. Coarse-grained molecular dynamics simulations support these predictions and show the induction of mobility inversion by multivalent counterions at dilute concentrations.
Article
Materials Science, Multidisciplinary
Yanzhou Wang, Zheyong Fan, Ping Qian, Miguel A. Caro, Tapio Ala-Nissila
Summary: In this study, the thermal transport properties of amorphous silicon were systematically investigated using large-scale molecular dynamics simulations. It was found that a simulation cell with up to 64,000 atoms and an appropriate quenching rate are required to achieve almost convergent thermal conductivity. The accuracy of the simulation method was verified by comparing structural properties and experimental results, and the importance of quantum effects in the calculated thermal conductivity was emphasized.
Article
Materials Science, Multidisciplinary
Enzo Granato, K. R. Elder, S. C. Ying, T. Ala-Nissila
Summary: In this study, the effects of thermal fluctuations and pinned boundaries in graphene membranes are investigated using a phasefield crystal model. The height fluctuations in systems with free boundaries exhibit linear diffusion behavior for long times, but still show subdiffusive behavior at intermediate times, consistent with experimental observations. Under compression, mirror buckling fluctuations are found, where the average height changes from above to below the pinned boundaries, and the average time between fluctuations diverges below a critical temperature corresponding to a thermally induced buckling transition. Near the transition, a nonlinear height response is observed, in agreement with recent renormalization group calculations and experimental results on graphene membranes under an external transverse force with clamped boundaries.
Article
Materials Science, Multidisciplinary
Rhodri Mansell, Yifan Zhou, Kassius Kohvakka, See-Chen Ying, Ken R. Elder, Enzo Granato, Tapio Ala-Nissila, Sebastiaan Van Dijken
Summary: This study demonstrates the formation of a weakly pinned skyrmion liquid in a magnetic heterostructure, and evaluates the dependence of skyrmion dynamics on the skyrmion size and density. The diffusion of skyrmions is found to be largest in dense liquids with small skyrmions. These findings are important for the design of probabilistic computing devices.
Article
Chemistry, Physical
Xiang Yang, Alberto Scacchi, Hossein Vahid, Maria Sammalkorpi, Tapio Ala-Nissila
Summary: We use the SPB theory to study the interaction between two parallel polyelectrolytes in monovalent ionic solutions. The theory accurately captures the interactions beyond the PE radius and accounts for positional correlations between charged groups. The results suggest that the SPB theory is an efficient way to model interactions in chemically specific complex PE systems.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Ryan R. Keogh, Santhan Chandragiri, Benjamin Loewe, Tapio Ala-Nissila, Sumesh P. Thampi, Tyler N. Shendruk
Summary: This research demonstrates that confining extensile nematics in 3D channels can lead to the emergence of two self-organized flow states with nonzero helicity. These states, a double helix and a grinder train, highlight the potential of active fluids in creating complex and organized spatiotemporal structures in 3D fluidic devices.
