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Żuk P.J., Słowicka A.M., Ekiel-Jeżewska M.L., Stone H.A.^{♦}, Universal features of the shape of elastic fibres in shear flow,
JOURNAL OF FLUID MECHANICS, ISSN: 0022-1120, DOI: 10.1017/jfm.2020.1048, Vol.914, pp.A31-1-41, 2021Abstract: We present a numerical study of the dynamics of an elastic fibre in a shear flow at low Reynolds number, and seek to understand several aspects of the fibre's motion using the equations for slender-body theory coupled to the elastica. The numerical simulations are performed in the bead-spring framework including hydrodynamic interactions in two theoretical schemes: the generalized Rotne-Prager-Yamakawa model and a multipole expansion corrected for lubrication forces. In general, the two schemes yield similar results, including for the dominant scaling features of the shape that we identify. In particular, we focus on the evolution of an initially straight fibre oriented in the flow direction and show that the time scales of fibre bending, curling and rotation, which depend on its length and stiffness, determine the overall motion and evolution of the shapes. We document several characteristic time scales and curvatures representative of the shape that vary as power laws of the bending stiffness and fibre length. The numerical results are further supported by an interpretation using an elastica model. Keywords: Stokesian dynamics, particle/fluid flow, slender-body theory Affiliations:
Żuk P.J. | - | IPPT PAN | Słowicka A.M. | - | IPPT PAN | Ekiel-Jeżewska M.L. | - | IPPT PAN | Stone H.A. | - | Princeton University (US) |
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2. |
Słowicka A.M., Stone H.A.^{♦}, Ekiel-Jeżewska M.L., Flexible fibers in shear flow approach attracting periodic solutions,
PHYSICAL REVIEW E, ISSN: 2470-0045, DOI: 10.1103/PhysRevE.101.023104, Vol.101, No.2, pp.023104-1-14, 2020Abstract: The three-dimensional dynamics of a single non-Brownian flexible fiber in shear flow is evaluated numerically, in the absence of inertia. A wide range of ratios A of bending to hydrodynamic forces and hundreds of initial configurations are considered. We demonstrate that flexible fibers in shear flow exhibit much more complicated evolution patterns than in the case of extensional flow, where transitions to higher-order modes of characteristic shapes are observed when A exceeds consecutive threshold values. In shear flow, we identify the existence of an attracting steady configuration and different attracting periodic motions that are approached by long-lasting rolling, tumbling, and meandering dynamical modes, respectively. We demonstrate that the final stages of the rolling and tumbling modes are effective Jeffery orbits, with the constant parameter C replaced by an exponential function that either decays or increases in time, respectively, corresponding to a systematic drift of the trajectories. In the limit of C→0, the fiber aligns with the vorticity direction and in the limit of C→∞, the fiber periodically tumbles within the shear plane. For moderate values of A, a three-dimensional meandering periodic motion exists, which corresponds to intermediate values of C. Transient, close to periodic oscillations are also detected in the early stages of the modes. Affiliations:
Słowicka A.M. | - | IPPT PAN | Stone H.A. | - | Princeton University (US) | Ekiel-Jeżewska M.L. | - | IPPT PAN |
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3. |
Farutin A.^{♦}, Piasecki T., Słowicka A.M., Misbah C.^{♦}, Wajnryb E., Ekiel-Jeżewska M.L., Dynamics of flexible fibers and vesicles in Poiseuille flow at low Reynolds number,
SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/c6sm00819d, Vol.12, pp.7307-7323, 2016Abstract: The dynamics of flexible fibers and vesicles in unbounded planar Poiseuille flow at low Reynolds number is shown to exhibit similar basic features, when their equilibrium (moderate) aspect ratio is the same and vesicle viscosity contrast is relatively high. Tumbling, lateral migration, accumulation and shape evolution of these two types of flexible objects are analyzed numerically. The linear dependence of the accumulation position on relative bending rigidity, and other universal scalings are derived from the local shear flow approximation. Keywords: Poiseuille flow, Stokes equations, vesicles, flexible fibers Affiliations:
Farutin A. | - | Université Grenoble Alpes (FR) | Piasecki T. | - | IPPT PAN | Słowicka A.M. | - | IPPT PAN | Misbah C. | - | CNRS (FR) | Wajnryb E. | - | IPPT PAN | Ekiel-Jeżewska M.L. | - | IPPT PAN |
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4. |
Jas G.S.^{♦}, Rentchler E.C.^{♦}, Słowicka A.M., Hermansen J.R.^{♦}, Johnson C.K.^{♦}, Middaugh C.R.^{♦}, Kuczera K.^{♦}, Reorientation Motion and Preferential Interactions of a Peptide in Denaturants and Osmolyte,
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN: 1520-6106, DOI: 10.1021/acs.jpcb.6b00028, Vol.120, pp.3089-3099, 2016Abstract: Fluorescence anisotropy decay measurements and all atom molecular dynamics simulations are used to characterize the orientational motion and preferential interaction of a peptide, N-acetyl-tryptophan-amide (NATA) containing two peptide bonds, in aqueous, urea, guanidinium chloride (GdmCl), and proline solution. Anisotropy decay measurements as a function of temperature and concentration showed moderate slowing of reorientations in urea and GdmCl and very strong slowing in proline solution, relative to water. These effects deviate significantly from simple proportionality of peptide tumbling time to solvent viscosity, leading to the investigation of microscopic preferential interaction behavior through molecular dynamics simulations. Examination of the interactions of denaturants and osmolyte with the peptide backbone uncovers the presence of strongest interaction with urea, intermediate with proline, and weakest with GdmCl. In contrast, the strongest preferential solvation of the peptide side chain is by the nonpolar part of the proline zwitterion, followed by urea, and GdmCl. Interestingly, the local density of urea around the side chain is higher, but the GdmCl distribution is more organized. Thus, the computed preferential solvation of the side chain by the denaturants and osmolyte can account for the trend in reorientation rates. Analysis of water structure and its dynamics uncovered underlying differences between urea, GdmCl, and proline. Urea exerted the smallest perturbation of water behavior. GdmCl had a larger effect on water, slowing kinetics and stabilizing interactions. Proline had the largest overall interactions, exhibiting a strong stabilizing effect on both water–water and water–peptide hydrogen bonds. The results for this elementary peptide system demonstrate significant differences in microscopic behavior of the examined solvent environments. For the commonly used denaturants, urea tends to form disorganized local aggregates around the peptide groups and has little influence on water, while GdmCl only forms specific interactions with the side chain and tends to destabilize water structure. The protective osmolyte proline has the strongest and most specific interactions with the tryptophan side chain, and also stabilizes both water–water and water–peptide hydrogen bonds. Our results strongly suggest protein or peptide denaturation triggered by urea occurs by direct interaction, whereas GdmCl interacts favorably with side chains and destabilizes peptide–water hydrogen bonds. The stabilization of biopolymers by an osmolyte such as proline is governed by favorable preferential interaction with the side chains and stabilization of water. Keywords: molecular dynamics simulations, fluorescence anisotropy, peptides, orientational motion Affiliations:
Jas G.S. | - | University of Kansas (US) | Rentchler E.C. | - | University of Kansas (US) | Słowicka A.M. | - | IPPT PAN | Hermansen J.R. | - | Central University of the Caribbean (US) | Johnson C.K. | - | University of Kansas (US) | Middaugh C.R. | - | University of Kansas (US) | Kuczera K. | - | other affiliation |
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5. |
Kuei S.^{♦}, Słowicka A.M., Ekiel-Jeżewska M.L., Wajnryb E., Stone H.A.^{♦}, Dynamics and topology of a flexible chain: knots in steady shear flow,
NEW JOURNAL OF PHYSICS, ISSN: 1367-2630, DOI: 10.1088/1367-2630/17/5/053009, Vol.17, pp.053009-1-15, 2015Abstract: We use numerical simulations of a bead–spring model chain to investigate the evolution of the conformations of long and flexible elastic fibers in a steady shear flow. In particular, for rather open initial configurations, and by varying a dimensionless elastic parameter, we identify two distinct conformational modes with different final size, shape, and orientation. Through further analysis we identify slipknots in the chain. Finally, we provide examples of initial configurations of an 'open' trefoil knot that the flow unknots and then knots again, sometimes repeating several times. Keywords: knots, low Reynolds number flows, multipole method Affiliations:
Kuei S. | - | Princeton University (US) | Słowicka A.M. | - | IPPT PAN | Ekiel-Jeżewska M.L. | - | IPPT PAN | Wajnryb E. | - | IPPT PAN | Stone H.A. | - | Princeton University (US) |
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6. |
Słowicka A.M., Wajnryb E., Ekiel-Jeżewska M.L., Dynamics of flexible fibers in shear flow,
JOURNAL OF CHEMICAL PHYSICS, ISSN: 0021-9606, DOI: 10.1063/1.4931598, Vol.143, pp.124904-1-6, 2015Abstract: Dynamics of flexible non-Brownian fibers in shear flow at low-Reynolds-number are analyzed numerically for a wide range of the ratios A of the fiber bending force to the viscous drag force. Initially, the fibers are aligned with the flow, and later they move in the plane perpendicular to the flow vorticity. A surprisingly rich spectrum of different modes is observed when the value of A is systematically changed, with sharp transitions between coiled and straightening out modes, period-doubling bifurcations from periodic to migrating solutions, irregular dynamics, and chaos. Keywords: Shear flows, Chaotic dynamics, Vortex dynamics, Numerical solutions, Periodic solutions Affiliations:
Słowicka A.M. | - | IPPT PAN | Wajnryb E. | - | IPPT PAN | Ekiel-Jeżewska M.L. | - | IPPT PAN |
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7. |
Słowicka A.M., Wajnryb E., Ekiel-Jeżewska M.L., Lateral migration of flexible fibers in Poiseuille flow between two parallel planar solid walls,
EUROPEAN PHYSICAL JOURNAL E, ISSN: 1292-8941, DOI: 10.1140/epje/i2013-13031-2, Vol.36, pp.1-12, 2013Abstract: Dynamics of non-Brownian flexible fibers in Poiseuille flow between two parallel planar solid walls is evaluated from the Stokes equations which are solved numerically by the multipole method. Fibers migrate towards a critical distance from the wall zc, which depends significantly on the fiber length N and bending stiffness A. This effect can be used to sort fibers. Three types of accumulation are found, depending on a shear-to-bending parameter Γ. In the first type, stiff fibers deform only a little and accumulate close to the wall, where their tendency to drift away from the channel is balanced by the repulsive hydrodynamic interaction with the wall. In the second type, flexible fibers deform significantly and accumulate far from the wall. In both types, the fiber shapes at the accumulation positions are repeatable, while in the third type, they are very compact and non-repeatable. The difference between the second and third accumulation types is a special case of the difference between the regular and irregular modes for the dynamics of migrating fibers. At the regular mode, far from walls, the fiber tumbling frequency satisfies Jeffery’s expression, with the local shear rate and the aspect ratio close to N. Keywords: Self-organisation, Supramolecular assemblies Affiliations:
Słowicka A.M. | - | IPPT PAN | Wajnryb E. | - | IPPT PAN | Ekiel-Jeżewska M.L. | - | IPPT PAN |
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8. |
Słowicka A.M., Ekiel-Jeżewska M.L., Sadlej K., Wajnryb E., Dynamics of fibers in a wide microchannel,
JOURNAL OF CHEMICAL PHYSICS, ISSN: 0021-9606, DOI: 10.1063/1.3678852, Vol.136, pp.044904-1-8, 2012Abstract: Dynamics of single flexible non-Brownian fibers, tumbling in a Poiseuille flow between two parallel solid plane walls, is studied with the use of the HYDROMULTIPOLE numerical code, based on the multipole expansion of the Stokes equations, corrected for lubrication. Fibers, which are closer to a wall, more flexible (less stiff) or longer, deform more significantly and, for a wide range of the system parameters, they faster migrate towards the middle plane of the channel. For the considered systems, fiber velocity along the flow is only slightly smaller than (and can be well approximated by) the Poseuille flow velocity at the same position. In this way, the history of a fiber migration across the channel is sufficient to determine with a high accuracy its displacement along the flow. Keywords: Stokes equations, flexible fiber, Poiseuille flow, solid walls Affiliations:
Słowicka A.M. | - | IPPT PAN | Ekiel-Jeżewska M.L. | - | IPPT PAN | Sadlej K. | - | IPPT PAN | Wajnryb E. | - | IPPT PAN |
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9. |
Adamczyk Z.^{♦}, Cichocki B.^{♦}, Ekiel-Jeżewska M.L., Słowicka A.M., Wajnryb E., Wasilewska M.^{♦}, Fibrinogen conformations and charge in electrolyte solutions derived from DLS and dynamic viscosity measurements,
JOURNAL OF COLLOID AND INTERFACE SCIENCE, ISSN: 0021-9797, DOI: 10.1016/j.jcis.2012.07.010, Vol.385, pp.244-257, 2012Abstract: Hydrodynamic properties of fibrinogen molecules were theoretically calculated. Their shape was approximated by the bead model, considering the presence of flexible side chains of various length and orientation relative to the main body of the molecule. Using the bead model, and the precise many-multipole method of solving the Stokes equations, the mobility coefficients for the fibrinogen molecule were calculated for arbitrary orientations of the arms whose length was varied between 12 and 18 nm. Orientation averaged hydrodynamic radii and intrinsic viscosities were also calculated by considering interactions between the side arms and the core of the fibrinogen molecule. Whereas the hydrodynamic radii changed little with the interaction magnitude, the intrinsic viscosity exhibited considerable variation from 30 to 60 for attractive and repulsive interactions, respectively. These theoretical results were used for the interpretation of experimental data derived from sedimentation and diffusion coefficient measurements as well as dynamic viscosity measurements. Optimum dimensions of the fibrinogen molecule derived in this way were the following: the contour length 84.7 nm, the side arm length 18 nm, and the total volume 470 nm3, which gives 16% hydration (by volume). Our calculations enabled one to distinguish various conformational states of the fibrinogen molecule, especially the expanded conformation, prevailing for pH < 4 and lower ionic strength, characterized by high intrinsic viscosity of 50 and the hydrodynamic radius of 10.6 nm. On the other hand, for the physiological condition, that is, pH = 7.4 and the ionic strength of 0.15 M NaCl, the semi-collapsed conformation dominates. It is characterized by the average angle equal to = 55, intrinsic viscosity of 35, and the hydrodynamic radius of 10 nm. Additionally, the interaction energy between the arms and the body of the molecule was predicted to be 4 kT units, confirming that they are oppositely charged than the central nodule. Results obtained in our work confirm an essential role of the side chains responsible for a highly anisotropic charge distribution in the fibrinogen molecule. These finding can be exploited to explain anomalous adsorption of fibrinogen on various surfaces. Keywords: Bead model of fibrinogen, Charge distribution over fibrinogen, Conformations of fibrinogen molecule, Fibrinogen molecule conformations, Hydrodynamic radius of fibrinogen, Viscosity of fibrinogen solutions Affiliations:
Adamczyk Z. | - | Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences (PL) | Cichocki B. | - | University of Warsaw (PL) | Ekiel-Jeżewska M.L. | - | IPPT PAN | Słowicka A.M. | - | IPPT PAN | Wajnryb E. | - | IPPT PAN | Wasilewska M. | - | other affiliation |
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10. |
Słowicka A.M., Walenta Z.A., Szymański Z., Expansion of a multi-component laser-ablated plume,
EUROPEAN PHYSICAL JOURNAL-APPLIED PHYSICS, ISSN: 1286-0042, DOI: 10.1051/epjap/2011110056, Vol.56, pp.11101-p1-8, 2011Abstract: The expansion of a plume generated during laser ablation is studied with the Direct Simulation Monte Carlo method. The plume is a mixture of four disparate molecular mass components and expands in vacuum or into ambient gas. The time dependence of deposition rate is studied and the transition from an initial vacuum-like to a diffusion-like regime of expansion in ambient gas is shown. The lack of stoichiometry increases with the ratio of molecular masses of ablated particles and at disparate masses the stoichiometry is seriously affected. Ambient gas worsens the stoichiometry unless it supplies particles compensating the backward and sideward flows of plume constituents. Keywords: laser deposition, plume expansion, DSMC Affiliations:
Słowicka A.M. | - | IPPT PAN | Walenta Z.A. | - | IPPT PAN | Szymański Z. | - | IPPT PAN |
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11. |
Słowicka A.M., Walenta Z.A., Creating thin layers at the contact surface of two nonmixing liquids,
BULLETIN OF THE POLISH ACADEMY OF SCIENCES: TECHNICAL SCIENCES, ISSN: 0239-7528, Vol.55, pp.173-178, 2007Abstract: The paper presents the results of numerical simulation of processes aimed at production of nanostructures with the use of oil emulsions in water. The appropriate molecular models of water and oil, as well as the model of the substance which would sediment at the water – oil interface, are looked for. Such substance, after suitable solidification, would become the main component of the produced material. For the described simulations, the Molecular Dynamics method has been used throughout this paper. Keywords: thin layers, contact surface, nonmixing liquids Affiliations:
Słowicka A.M. | - | IPPT PAN | Walenta Z.A. | - | IPPT PAN |
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12. |
Słowicka A.M., Walenta Z.A., Powstawanie nanostruktur w emulsjach,
Systems, Vol.11, pp.255-267, 2006Abstract: Współczesne technologie materiałowe są jedną z najszybciej rozwijających się dziedzin nauki i techniki. Szczególnie prężnie rozwijaj się nano- i mikrotechnologie. Jedna z takich nowoczesnych nanotechnologii, badana obecnie w kilku europejskich ośrodkach, wykorzystuje efekt gromadzenia się substancji na granicy faz emulsji. Użyta emulsja ma bardzo drobną strukturę nano-kropli oleju w wodzie. Trzecia substancja, dzięki odpowiednim właściwościom molekularnym, osiadając na powierzchni styku faz cieczy pokrywa powierzchnie kropel oleju. Po usunięciu emulsji substancja ta, zachowując strukturę, zostaje utwardzona i tworzy nano-materiał. W prezentowanej technologii emulsja spełnia rolę matrycy, na której powstaje struktura wytwarzanego materiału. Technik rozdrabniania emulsji jest wiele; stosuje się m.in. aparaty miksujące (homogenizatory), które w przepływie ścinającym rozrywają krople oleju na mniejsze lub mikrokanały o podobnym działaniu [2]. Nanomateriały o prezentowanej strukturze będą miały wiele interesujących właściwości, takich jak lekkość, elastyczność czy wytrzymałość mechaniczną, co zapewniają silne oddziaływania międzyatomowe w układzie oraz porowatość substancji. Tworzywa o takiej budowie mogą znaleźć zastosowanie w różnych dziedzinach np. medycynie czy aerodynamice. Celem naszych prac nad omawianą technologią wytwarzania nanomateriałów było stworzenie numerycznego modelu zjawiska powstawania nanostruktur w emulsjach. Ponieważ tak drobne układy wymagają modelowania na poziomie atomowym, do opisu procesów zachodzących w cieczach posłużono się metodą Dynamiki Molekularnej. Bazując na symulacjach numerycznych zbudowano modele molekularne cieczy tworzących emulsję oraz zaproponowano kilka typów substancji, które mogłyby wytworzyć pożądaną warstwę na granicy faz. Zaproponowane modele testowano numerycznie, poszukując kombinacji oddziaływań międzyatomowych zapewniającej powstawanie oczekiwanej nanostruktury Keywords: nanostruktury, emulsje, nanomateriały Affiliations:
Słowicka A.M. | - | IPPT PAN | Walenta Z.A. | - | IPPT PAN |
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