Dynamics Computer Simulations Research Articles

Cooperative dynamics of PARP-1 zinc-finger domains in the detection of DNA single-strand breaks

The DNA single-strand break (SSB) repair pathway is initiated by the multifunctional enzyme PARP-1, which recognizes the broken DNA ends by its two zinc-finger domains, Zn1 and Zn2. Despite a number of experiments performed with different DNA configurations and reduced fragments of PARP-1, many details of this interaction that is crucial to the correct initiation of the repair chain are still unclear. We performed Molecular Dynamics (MD) computer simulations of the interaction between the Zn1/Zn2 domains of PARP-1 and a DNA hairpin including a missing nucleotide to simulate the presence of an SSB, a construct used in recent experiments. The role of Zn1 and Zn2 interacting with the SSB ends is studied in detail, both independently and cooperatively. We also explored, PARP-1 operating as a dimer, with the two Zn-fingers coming from two separate copies of the enzyme. By an extensive set of all-atom molecular simulations employing state-of-the art force fields, assisted by empirical docking and free-energy calculations, we conclude that the particular conformation of the DNA hairpin can indeed spontaneously open up by thermal fluctuations, up to extremely kinked deformations. However, such extreme localized deformations are rarely observed in free, long DNA fragments. Protein side-loops make contact with the DNA hairpin grooves, and help Zn2 to penetrate deep in the SSB gap. In this way, Zn2 can interact with the nucleotides opposite to the missing base. Overall, Zn1 plays a secondary role: the crucial factor for the interaction is rather the relative arrangement of the Zn1/Zn2 couple, and their mutual orientation with respect to the 3′\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$3'$$\\end{document} and 5′\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$5'$$\\end{document} SSB end terminals. This helps to obtain an early interacting configuration, which ultimately leads to molecular PARP-1-DNA structures similar to those observed experimentally. Such findings represent an important step toward defining the detailed function of PARP-1 in the early stages of SSB recognition.

The structural and electronic configuration of an amorphous silica surface, from its liquid to glassy state

Through classical molecular dynamics computational simulations, the surface of amorphous silica (vitreous silica) was generated for a system comprising 64 SiO2 molecules (192 atoms) via the classical three-body glass potential. Starting from the liquid state of silica at 3400 K, it was cooled in three different ways at intervals of 200, 400, and 2000 K, with a cooling rate of 4.4 K/ps and establishing relaxation at intermediate temperatures, yielding three groups of surfaces from 3400 to 1400 K. Subsequently, these systems underwent sudden cooling from 1400 to 300 K via the Andersen and Nosé‒Hoover thermostats, followed by relaxation at 300 K via a microcanonical ensemble (NVE constant). Each surface that underwent relaxation was analyzed through ab initio molecular dynamics for the following three physical properties, which are temperature dependent. The average electric charges of oxygen and silicon. Microstructures on the outermost part of the surface were observed and comprised nonbridging oxygen atoms, undercoordinated silicon, and N-membered rings (3 ≤ N ≤ 5). The radial distribution functions were analyzed for all surfaces. Below 2000 K, a type of freezing is observed in all the structures because of the glass transition. All analyses were performed at zero pressure.

Thermal Transport and Thermal Polarization of Water in the Supercooled Regime.

The behavior of water in the deep supercooled regime has attracted significant interest, motivated by the hypothesis of the second critical point of water. Previous studies indicated the existence of a water anomaly, characterized by a minimum in the thermal conductivity of water. Here, we employ nonequilibrium molecular dynamics computer simulation and the TIP4P/2005 water force field to investigate the thermal conductivity of supercooled water targeting four different isobars, 1, 200, 700, and 1200 bar. We demonstrate using NEMD simulations the existence of minima in thermal conductivity associated with the maximum isothermal compressibility and the minimum speed of sound in water, hence establishing a firm connection with the second critical point of liquid water. Moreover, we demonstrate that thermal gradients polarize supercooled water with a thermal polarization coefficient of several mV/K. We explain the thermal polarization effect using a theoretical formulation introduced recently that connects the thermal polarization effect to the isobaric thermal expansion coefficient.

Nonequilibrium relaxation of soft responsive colloids.

Stimuli-responsive macromolecules display large conformational changes during their dynamics, sometimes switching between states. Such a multi-stability is useful for the development of soft functional materials. Here, we introduce a mean-field dynamical density functional theory for a model of responsive colloids to study the nonequilibrium dynamics of a colloidal dispersion in time-dependent external fields, with a focus on the coupling of translational and conformational dynamics during their relaxation. Specifically, we consider soft Gaussian particles with a bimodal size distribution between two confining walls with time-dependent (switching-on and off) external gravitational and osmotic fields. We find a rich relaxation behavior of the systems in excellent agreement with particle-based Brownian dynamics computer simulations. In particular, we find time-asymmetric relaxations of integrated observables (wall pressures, mean size, and liquid center-of-mass) for activation/deactivation of external potentials, respectively, which are tunable by the ratio of translational and conformational diffusion time scales. Our work thus paves the way for studying the nonequilibrium relaxation dynamics of complex soft matter with multiple degrees of freedom and hierarchical relaxations.

How norms shape the evolution of prosocial behaviour–compassion, universalizability, reciprocity and equity: a C.U.R.E for social dilemmas

How cooperation evolves and persists widely remains an open problem for improving humanity across domains ranging from climate change to pandemic response. To shed light on how behavioural norms can resolve social dilemmas around cooperation, we present a formal mathematical model of individuals’ decision making under general social norms, encompassing a variety of concerns and motivations an individual may have beyond simply maximizing their own payoff. Using the canonical Prisoner’s dilemma, we compare four norms: compassion, universalizability, reciprocity and equity, to determine which, if any, social forces can facilitate the evolution of cooperation. We analyse our model through a variety of limiting cases, including weak selection, low mutation and large population sizes. This is complemented by computer simulations of population dynamics via a Fisher process, which confirm our theoretical results. We find that the first two norms lead to the emergence of cooperation in a wide range of games, but the latter two cannot. Owing to our framework’s generality, it can be used to investigate many other norms, and how norms themselves evolve. Our work complements recent work on fair-minded learning dynamics and provides a useful bottom-up perspective into understanding the impact of top-down social norms on collective cooperative intelligence.

Abstract We068: TRAF6 Mediates TFEB Ubiquitination to Inhibit Cardiomyocyte Autophagy in Sepsis-Associated Cardiac Dysfunction

Sepsis-associated cardiac dysfunction (SACD) is the predominant cause of death in patients with severe sepsis. Complex mechanisms have been proposed for SACD, including maladaptive inflammation and autophagy. However, studies in the past have emphasized these different manifestations underlying SACD as discrete processes and largely neglect their inherent connection. Herein using both in vivo and in vitro SACD models, we showed that the cardiomyocyte Toll-like receptor 4 (cTLR4) can serve as a key receptor mediating the interaction between the cardiomyocyte and macrophage under SACD-like conditions. The stress-induced secretome of macrophage caused activation of cTLR4 which intensified the impairment of autophagic flux in cardiomyocytes. The TNF receptor-associated factor 6 (TRAF6) was further identified as the primary downstream target which conferred the regulatory effects of TLR4 signaling on cardiac autophagy. Importantly, we found that cardiac targeted Traf6 gain-of function exacerbated, while cardiac targeted Traf6 loss-of function partially rescued, the cardiac dysfunction in a mice model of SACD. Mechanistically, TRAF6 functioned as a ubiquitin E3 ligase to facilitate the degradation of transcription factor EB (TFEB) via ubiquitination and subsequently led to the blockage of autophagic flux. Along the line, dynamics computational simulation combined with experimental validation revealed unique local electrostatic interactions between human TRAF6 and TFEB. Overall, our study provides novel mechanistic supports which link the macrophage-initiated inflammation and cardiomyocyte autophagy, demonstrates a previously undescribed role of cTLR4/TRAF6/TFEB signaling in fine-tuning cardiac autophagy, and highlights TRAF6 as a novel therapeutic gene target to develop autophagy-based therapeutics for SACD.

Computer Simulation for Effective Pharmaceutical Kinetics and Dynamics: A Review.

Computer-based modelling and simulation are developing as effective tools for supplementing biological data processing and interpretation. It helps to accelerate the creation of dosage forms at a lower cost and with the less human effort required to conduct the work. This paper aims to provide a comprehensive description of the different computer simulation models for various drugs along with their outcomes. The data used are taken from different sources, including review papers from Science Direct, Elsevier, NCBI, and Web of Science from 1995-2020. Keywords like - pharmacokinetic, pharmacodynamics, computer simulation, whole-cell model, and cell simulation, were used for the search process. The use of computer simulation helps speed up the creation of new dosage forms at a lower cost and less human effort required to complete the work. It is also widely used as a technique for researching the structure and dynamics of lipids and proteins found in membranes. It also facilitates both the diagnosis and prevention of illness. Conventional data analysis methods cannot assess and comprehend the huge amount, size, and complexity of data collected by in vitro, in vivo</i>, and ex vivo</i> experiments. As a result, numerous in silico</i> computational e-resources, databases, and simulation software are employed to determine pharmacokinetic (PK) and pharmacodynamic (PD) parameters for illness management. These techniques aid in the provision of multiscale representations of biological processes, beginning with proteins and genes and progressing through cells, isolated tissues and organs, and the whole organism.

Polyampholytes with Various Charge Distributions: Conformation States via Computer Simulation.

By means of molecular dynamics computer simulation, the conformational space of polyampholyte macromolecules with various distributions of the charged groups along the chain is studied. A coarse-grained model where each monomer unit of the chain is presented as a non-charged group in the backbone of the macromolecule connected with a charged side pendant is considered. A limiting case of fully charged chains in the isoelectric point is investigated. The oppositely charged monomer units are distributed in various patterns: regular alternating, multiblock, or random sequences. It is found that the chains with random unit distribution adopt much more compacted conformations than the chains with regular distributions with comparable block lengths. Calculating the chain size and its fluctuation along with the spatial density distribution, coil, and globular conformations are distinguished and arranged on the diagrams in terms of chain length, block length, and Bjerrum length.

Going beyond an old shockwave conjecture for improving upon Navier-Stokes.

Nonequilibrium molecular dynamics (NEMD) computer simulations of steady shockwaves in dense fluids and rarefied gases produce detailed shockwave profiles of mechanical and thermal properties. The Boltzmann equation, under the assumption of local thermodynamic equilibrium (LTE), leads to the first-order (linear) continuum theory of hydrodynamic flow: Navier-Stokes-Fourier (NSF). (Expansion of the LTE Boltzmann equationin higher powers of gradients yields so-called Burnett second-order terms, etc.) NEMD simulations of strong shockwaves with high gradients are not well modeled by NSF theory. Many years ago, a conjecture for going "beyond Navier-Stokes" was proposed, applying the empirical observation of anisotropic thermal enhancement in the shock front to the temperature dependence of the NSF transport coefficients, whose dissipation determines the slope at the center of the shock profile: for weak shocks, the actual coefficients in NEMD simulations appear to be smaller than in NSF predictions, leading to steeper gradients being observed, while for strong shocks, the NEMD coefficients appear to be larger, leading to less steep shock rises than predicted by NSF calculations. In this paper, we show that adding significant Burnett nonlinearity into an LTE continuum theory reproduces the early shock rise and slope of NEMD profiles, for both weak and strong shocks in dense fluids, as well as strong shockwaves in the ideal gas. Moreover, we show that "Holian's conjecture" incorporates significant Burnett nonlinearity, but like all the other LTE continuum theories, it fails to describe the slow NEMD return to equilibrium beyond the shock front. We show that Maxwell relaxation has to be applied to the hydrodynamic variables themselves (rather than attempting indirect relaxation of their gradients) in order to more accurately model the entire shockwave profile. Non-LTE Maxwell relaxation is the only way to bring the entire profile into agreement with NEMD, most noticeably for strong shockwaves.

Unification of Ewald and shifted force methods to calculate Coulomb interactions in molecular simulations.

Three new Ewald series are derived using a new strategy that does not start with a proposed charge spreading function. Of these, the Ewald series produced using shifted potential interactions for the Ewald real space series converges relatively slowly, while the corresponding expression using a shifted force (SF) interaction does not converge. A comparison is made between several approximations of the Ewald method and the SF route to include Coulomb interactions in molecular dynamics (MD) computer simulations. MD simulations of a model bulk molten salt and water were carried out. The recently derived α' variant of Ewald, by K. D. Hammonds and D. M. Heyes [J. Chem. Phys. 157, 074108 (2022)], has been developed analytically and found to be more accurate and computationally efficient than SF in part due to the smaller real space truncation distance that can be used. In addition, with α', the number of reciprocal lattice vectors required is reduced considerably compared with the standard Ewald implementations to give the same accuracy. The invention of the α' method shifts the computational balance back toward using an Ewald construction. The SF method shows greater errors in the Coulomb pressure and time dependent fluctuation properties compared to α'. It does not conserve the shadow Hamiltonian in a microcanonical MD simulation, whereas the α' method does, which facilitates long time stability and insignificant drift of properties over time. The speed of the Ewald computer code is improved by using a new lookup table method.

Influence of Nanoparticles in Lubricant on Sliding Contact of Atomic Rough Surfaces—A Molecular Dynamics Study

In this work, large-scale molecular dynamics (MD) computational simulations were performed in order to explore the sliding contact responses of rough surfaces with hexadecane lubricant and added nanoparticles. Simulation results revealed that the frictional state was dependent on the fluid, nanoparticle, and surface roughness. Three lubricating conditions were compared based on considerations of different amounts of fluid molecules. The lubricant was not able to separate the frictional contact surfaces if the quantity of lubricant molecules was insufficient. Particularly, there were no lubricating contributions when the amount of lubricant was too low, and the lubricant therefore only filled the pits in the surface roughness. Thus, the normal load was primarily supported by the contact between the two surfaces and nanoparticles, leading to significant surface morphology changes. In contrast, the frictional contact surfaces were able to be completely separated by the lubricant when there was a sufficient amount of fluid, and a very good lubricating effect could thus be achieved, resulting in a smaller friction force. In addition, the changes in surface morphology, contact area, and RMS are discussed in this paper, in order to reveal the dynamic frictional process.

All in one doubly pillared MXene membrane for excellent oil/water separation, pollutant removal, and anti-fouling performance

Given the diversity and complexity of coexisting oil/dyes/heavy metal ions/microorganisms in wastewater and volatile organic compounds (VOCs) in the air, developing separation materials featured in higher separation efficiency and lower energy consumption for oil and water separation, pollutant removal, and anti-fouling is urgently needed, but it remains a major challenge till now. Herein, a multifunctional Ti3C2 MXene membrane with unique double pillar support was proposed by liquid phase ultrasonication and vacuum filtration to overcome the above challenge. Introducing cetyl-trimethyl ammonium bromide (CTAB) and calcium chloride/sodium alginate (CaCl2/SA) to the MXene membrane as crossed double pillars and superhydrophilic surface increases the tolerance and wettability of the membrane. The fabricated doubly pillared MXene (d-Ti3C2) membrane exhibits superior oil/water (O/W) separation efficiency (99.76%) with flux (1.284 L m−2 h−1) for canola oil and organic dye removing efficiency for methyl blue (MB) 99.85%, malachite green (MG) 100%, and methyl violet (MV) 99.72%, respectively, which is 1.05, 1.44, 1.22, and 1.28 fold compared with pre-pillared Ti3C2 (p-Ti3C2). The superior anti-oil/dye/fouling is attributed to lower oil conglutination, high hydrophily, and antibacterial activity. The versatile MXene membrane also shows distinguished separation of VOCs (η > 99%) from polluted air. The experimental and molecular dynamics (MD) computational simulation results illustrate that the superior separation efficiency of the Ti3C2 MXene membrane is ascribed to the unique doubly pillared space channel. This study paves a new road to further research on one step integration strategy for complex O/W separation, wastewater and VOCs removal, and anti-fouling via tuning nano/macro architecture.

Industrial environmental control of polycyclic aromatic hydrocarbons in organic fuel combustion product

RELEVANCE of this study lies in the computational justification of the choice of the installation location of a multipoint sampling probe in the measuring section of the flue of boiler plants of energy enterprises and thermal power plants that have a significant negative impact of emissions on the environment, in order to increase the reliability and representativeness ofinstrumental measurements during industrial environmental control (PEC) of polluting emissions (PE). PURPOSE. Improving the environmental safety of thermal power plants in the current conditions of the introduction of state principles of technological regulation of emissions is associated with the establishment of technological emission indicators for each source of atmospheric pollution at energy enterprises with a significant negative impact on the environment. In this regard, energy enterprises should carry out round-the-clock monitoring of PE, which requires reliable instrumental control of the content of marker substances in the combustion products of power boilers by determining a representative sampling point on the flue or chimney of an energy boiler installation. METHODS. The paper uses methods of computer simulation of gas dynamics to determine the local fields of concentration of PE and flow velocity and assess their unevenness in the flue of an energy boiler. RESULTS. Using the example of an operating energy boiler plant of a thermal power plant, a control section of the flue was determined to ensure industrial environmental control of marker substances in the combustion products of organic fuels. The average values of the concentration of PE and the flow rate of combustion products of local fields in the calculated sections and their values on the longitudinal axis of the boiler flue are determined, and their uneven distribution is estimated. CONCLUSION. The obtained research results can be used at energy enterprises and thermal power plants to justify the choice of a control representative measuring section for conducting a PEC, and to develop an environmental efficiency improvement program (EEIP).

Sequential Computer Simulation of H-minus Ion Dynamics from Source to RFQ Exit with Beam Rotation

An end-to-end simulation of the beam dynamics in the system of extraction, beam transportation and the first section of the accelerator (RFQ) is carried out. The proposed method of modeling the dynamics of ions from the source to the exit from the RFQ made it possible to quickly and efficiently change the parameters of the matching system depending on the final results of the beam passing into the RFQ. A system for matching a beam of negative hydrogen ions has been developed and optimized, which makes it possible to rotate the beam to block the propagation of cesium into the accelerator channel and to match the beam with RFQ. As a result of optimization of the matching channel, it is possible to obtain an emittance increase in RFQ of no more than 25 % for 90 % of the beam fraction, while the capture of beam particles in the acceleration mode is 98 % of the injected beam. The increased drifts in the matching system leave enough space for the placement of diagnostic equipment, a vacuum system and a beam correction system. The dependence of the beam dynamics in the RFQ on the charge distribution over the beam cross section at the output of the matching channel is established.

Experimental and theoretical fluid dynamics of spherical Savonius turbines operated in pipe flows

The performance of Savonius turbines driven by flow in a pipe is experimentally investigated. The turbine is manufactured to have a spherical outline based on the pipe cross section at a small clearance. The torque and power of the turbine are obtained from the time derivative of the rotational speed measured using a high-speed camera and an equation of rotational motion. We find that the idling tip-speed ratio of the turbine exceeds 5, which is much greater than that of a turbine operating in an open free stream. This proves the dominance of pulsatile flow through the gap between two hemispherical blades in torque generation. Widely varying the gap (i.e., the overlap ratio OR of the Savonius turbine) reveals that a turbine with OR = 30 % has the highest power coefficient. The output efficiency exceeds 50 % for a tip-speed ratio of approximately 3. These experimental results are supported by fluid dynamics theory and computational fluid dynamics simulation, which clarify the driving mechanism of the turbine in a pipeline.

Experimental examination of dipole-dipole cross-correlations by dielectric spectroscopy, depolarized dynamic light scattering, and computer simulations of molecular dynamics.

The contribution of cross- and self-correlations to the dielectric and light-scattering spectra of supercooled polar glass formers has recently become a most challenging problem. Herein, we employ dielectric spectroscopy, depolarized dynamic light scattering (DDLS), and rheology to thoroughly examine the dynamics of van der Waals liquid 1,2-Diphenylvinylene. Carbonate (DVC), which is a polar counterpart of canonical glass former ortho-Terphenyl (OTP). We show that the light-scattering data correspond well with the dielectric permittivity function over a wide T range. This pattern is very different from the peaks' separation ω_{max}^{DDLS}/ω_{max}^{BDS}=3.7 reported recently for tributyl phosphate (TBP), despite the same dielectric characteristics of these two glass formers (β_{KWW}=0.75,Δɛ=20 for both TBP and DVC; KWW stands for Kohlrausch-Williams-Watts). This indicates different influence of orientational correlations in both methods for these two systems. We also show the results of the computer simulations of the model, polar molecules, which clearly indicate that the contribution of the cross-term to the correlation function probed in the DDLS experiment can be significant.

Local Structure of Atactic Polystyrene Investigated by Molecular Dynamics Method

Molecular dynamics computer simulation of three substances ethylbenzene (EB), pentastyrene (PS-5), and polystyrene-25 (PS-25) was performed to investigate the local order of the phenyl rings in monomers and side-chain polymers. Monomer molecules (EB) tend to be in T-configuration, which corresponds to isotropic local structure. Phenyl rings in chained molecules PS-5 and PS-25 partly cooperate in both parallel-displaced and “sandwich” configuration with π–π stacking. These configurations are locally anisotropic and lead to the increasing of Kerr constant K. Analysis of the local structure was performed by calculating the cylindrical distribution function.

Atomistic Computer Simulations of Uranyl Adsorption on Hydrated Illite and Smectite Surfaces

A quantitative understanding of the molecular-scale mechanisms of radionuclide sorption on different clay minerals is crucial for the development and safe implementation of geological nuclear waste disposal technologies. We apply classical molecular dynamics (MD) computer simulations to study the adsorption of uranyl on the external basal surfaces of two typical clay models. In the illite model, negative charge is primarily localized in the tetrahedral sheets, while in the lower-charge smectite model, the isomorphic substitutions are introduced in the octahedral sheet. The comparison of atomic density distributions at the clay surfaces and adsorption-free energies profiles as a function of distance from these surfaces demonstrates that overall U behavior at the basal clay surface is quite similar for illite and smectite. Uranyl is sorbed as a mixture of outer-sphere aqua complexes [UO2(H2O)5]2+ and hydrolyzed aqua complexes [UO2(H2O)4–5OH]+ on both surfaces. The structural and compositional differences between the models do not greatly affect the uranyl’s nearest coordination environment and are mainly reflected in the specific localization and orientation of the uranyl ions at both surfaces and in the magnitude of the adsorption-free energies. The observed quantitative characteristics of uranyl interactions with illite and smectite surfaces will help to better understand U behavior during the sorption process on clay minerals for the entire range of mixed-layer illite–smectite structures. A comparison of two versions of the ClayFF force field in the simulations made it possible to more accurately and quantitatively evaluate some subtle features of the uranyl–clay interactions and to obtain a more precise composition of uranyl complex with the modified ClayFF force field (ClayFF-MOH).

A Passive Polycentric Mechanism to Improve Active Mediolateral Balance in Prosthetic Walking.

Prosthetic legs are typically passive systems without active ankle control, restricting mediolateral balancing to a hip strategy. Resulting balance control impairments for persons with a lower extremity amputation may be mitigated by increasing hip strategy effectiveness, in which relatively small hip moments of force are adequate for mediolateral balancing. To increase hip strategy effectiveness we have developed a prosthetic leg prototype based on the Peaucellier mechanism, the Sideways Balance Mechanism (SBM). This polycentric mechanism adds a frontal plane degree of freedom, reducing mediolateral body displacements. Adding a passive joint alone introduces instability, in which mediolateral body rotation leads to CoM height loss, ultimately resulting in a fall. The SBM however provides stability typically absent by lengthening under rotation, thereby compensating for CoM height loss. By allowing for both foot rotation (in-/eversion), and increased mediolateral ground reaction force the SBM increases hip strategy effectiveness. We aimed to provide proof of principle that the SBM can improve active mediolateral balance control in prosthetic walking by increasing hip strategy effectiveness compared to a typical set-up. Comparison between a typical set-up and the SBM showed an increased mediolateral ground reaction force at equal hip moments of force for a 2D forwards dynamics computer simulation, and a reduced hip moment of force at equal mediolateral ground reaction force for a case study. Results validate increased hip strategy effectiveness of the SBM compared to a typical set-up, providing proof of principle that adding an SBM to a prosthetic set-up improves mediolateral balance control in prosthetic walking.

Mobilization in two-step capillary isoelectric focusing: Concepts assessed by computer simulation.

The mobilization step in a two-step capillary isoelectric focusing protocol is discussed by means of dynamic computer simulation data for systems without and with spacer compounds that establish their zones at the beginning and end of the focusing column. After focusing in an electroosmosis-free environment (first step), mobilization (second step) can be induced electrophoretically, by the application of a hydrodynamic flow, or by a combination of both means. Dynamic simulations provide insight into the complexity of the various modes of electrophoretic mobilization and dispersion associated with hydrodynamic mobilization. The data are discussed together with the relevant literature.