Agnieszka Słowicka, Ph.D. 

Doctoral thesis
20081030  Badanie metodą dynamiki molekularnej powstawania wybranych nanostruktur w emulsjach
 616 
Recent publications
1.  Farutin A.^{♦}, Piasecki T., Słowicka A.M., Misbah C.^{♦}, Wajnryb E., EkielJeżewska M.L., Dynamics of flexible fibers and vesicles in Poiseuille flow at low Reynolds number, SOFT MATTER, ISSN: 1744683X, DOI: 10.1039/c6sm00819d, Vol.12, pp.73077323, 2016 Abstract: 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:
 
2.  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: 15206106, DOI: 10.1021/acs.jpcb.6b00028, Vol.120, pp.30893099, 2016 Abstract: Fluorescence anisotropy decay measurements and all atom molecular dynamics simulations are used to characterize the orientational motion and preferential interaction of a peptide, Nacetyltryptophanamide (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:
 
3.  Kuei S.^{♦}, Słowicka A.M., EkielJeżewska M.L., Wajnryb E., Stone H.A.^{♦}, Dynamics and topology of a flexible chain: knots in steady shear flow, NEW JOURNAL OF PHYSICS, ISSN: 13672630, DOI: 10.1088/13672630/17/5/053009, Vol.17, pp.053009115, 2015 Abstract: 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:
 
4.  Słowicka A., Wajnryb E., EkielJeżewska M.L., Dynamics of flexible fibers in shear flow, JOURNAL OF CHEMICAL PHYSICS, ISSN: 00219606, DOI: 10.1063/1.4931598, Vol.143, pp.12490416, 2015 Abstract: Dynamics of flexible nonBrownian fibers in shear flow at lowReynoldsnumber 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, perioddoubling bifurcations from periodic to migrating solutions, irregular dynamics, and chaos. Keywords:Shear flows, Chaotic dynamics, Vortex dynamics, Numerical solutions, Periodic solutions Affiliations:
 
5.  Słowicka A.M., Wajnryb E., EkielJeżewska M.L., Lateral migration of flexible fibers in Poiseuille flow between two parallel planar solid walls, EUROPEAN PHYSICAL JOURNAL E, ISSN: 12928941, DOI: 10.1140/epje/i2013130312, Vol.36, pp.112, 2013 Abstract: Dynamics of nonBrownian 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 sheartobending 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 nonrepeatable. 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:Selforganisation, Supramolecular assemblies Affiliations:
 
6.  Słowicka A.M., EkielJeżewska M.L., Sadlej K., Wajnryb E., Dynamics of fibers in a wide microchannel, JOURNAL OF CHEMICAL PHYSICS, ISSN: 00219606, DOI: 10.1063/1.3678852, Vol.136, pp.04490418, 2012 Abstract: Dynamics of single flexible nonBrownian 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:
 
7.  Adamczyk Z.^{♦}, Cichocki B.^{♦}, EkielJeżewska M.L., Słowicka A., 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: 00219797, DOI: 10.1016/j.jcis.2012.07.010, Vol.385, pp.244257, 2012 Abstract: 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 manymultipole 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 semicollapsed 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:
 
8.  Słowicka A.M., Walenta Z.A., Szymański Z., Expansion of a multicomponent laserablated plume, EUROPEAN PHYSICAL JOURNALAPPLIED PHYSICS, ISSN: 12860042, DOI: 10.1051/epjap/2011110056, Vol.56, pp.11101p18, 2011 Abstract: 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 vacuumlike to a diffusionlike 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:
 
9.  Słowicka A., Walenta Z.A., Creating thin layers at the contact surface of two nonmixing liquids, BULLETIN OF THE POLISH ACADEMY OF SCIENCES: TECHNICAL SCIENCES, ISSN: 02397528, Vol.55, pp.173178, 2007 Abstract: 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:
 
10.  Słowicka A., Walenta Z.A., Powstawanie nanostruktur w emulsjach, Systems, Vol.11, pp.255267, 2006 Abstract: 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 nanokropli 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 nanomateriał . 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:

List of chapters in recent monographs
1. 549  Słowicka A.M., Walenta Z.A., Hoffman J., Chrzanowska J., Mościcki T., 30th International Symposium on Shock Waves 2, rozdział: Structure and Expansion of a Plume Emitted During Laser Ablation of Multicomponent Materials, Springer International Publishing AG 2017, 2, pp.869873, 2017 
Conference papers
1.  Walenta Z.A., Słowicka A.M., Detonation Waves in Narrow Channels of Various Shapes, ISIS23, 23rd International Shock Interaction Symposium, 20180709/0713, SKUKUZA REST CAMP (ZA), pp.135140, 2018 Abstract: One of the important contemporary technological problems is connected with necessity of extinguishing detonation, which may occur in pipelines transporting gaseous fuels. To achieve this goal usually a matrix of very narrow channels is placed inside the pipeline, perpendicularly to its axis. In our recent paper (Walenta and Slowicka (2016)) we have shown, that channels with sharp changes of crosssection should be more eﬃcient in this respect than traditionally used straight channels with constant crosssection area. In this paper we demonstrate how detonation behaves in the channels, in which gas ﬂows under realistic conditions – when friction and heat exchange are present. We take into account the fact, that gas ﬂowing through such channels accelerates and its density decreases considerably. Keywords:detonation waves, detonation damping, narrow channels Affiliations:
 
2.  Walenta Z.A., Słowicka A.M., Structure of shock waves in noble gases under high density conditions, ISSW31, 31st International Symposium on Shock Waves, 20170709/0714, Nagoya (JP), No.SBM000360, pp.16, 2017 Abstract: In the present paper we show the dependence of the shock structure in a dense, noble gas on each of the three nondimensional parameters: nondimensional initial density, nondimensional initial temperature and nondimensional shock velocity. It will also be demonstrated, that the length scale, most suitable for measuring the thickness of the shock wave in a dense gas, is the sum of the mean free path (calculated the same way as for a dilute gas) and the diameter of a single gas molecule. Affiliations:
 
3.  Walenta Z.A., Słowicka A.M., Extinguishing detonation in pipelines – optimization of the process, ISIS 2016, 22nd International Shock Interaction Symposium, 20160704/0708, Glasgow (GB), pp.15, 2016 Abstract: The necessity of extinguishing detonation, which may occur in pipelines transporting gaseous fuels, is nowadays a very important technological problem. The standard devices used for it consist of matrices of very narrow channels. Cooling the gas by cold walls of such channels may extinguish the flame and stop detonation. Detonation may also be extinguished if the crosssection of the channel transporting gas increases abruptly at some place. The desired effect may be achieved if the generated rarefaction waves decrease sufficiently the temperature of the flame (Teodorczyk et al. 1988, Cai et al. 2002, Dremin 1999, Walenta et al. 2004). It might be expected, that simultaneous use of both methods – using narrow channels with variable crosssection – should give even better results. Additional profit might come from the fact, that the flow in narrow channels is usually laminar; the abrupt increase of the crosssection would introduce some turbulence and this way enhance cooling by the walls. However, if the crosssection of the channel increases and decreases, the unwanted heating of the gas may occur. To estimate the net esult, which is not obvious, it is necessary to perform suitable simulations and experiments. The present paper is devoted to numerical simulation of the phenomenon. Keywords:extinguishing detonation, DSMC Affiliations:
 
4.  Walenta Z.A., Słowicka A., Structure of shock waves in complex molecular liquids, 29th International Symposium on Shock Waves, 20130714/0719, Madison (US), pp.14371441, 2013 Abstract: The present paper is a continuation of our earlier work on the molecular dynamics simulations, complex liquids, shock waves Affiliations:
 
5.  Walenta Z.A., Słowicka A.M., Structure of shock waves in dense gases and liquids  Molecular Dynamics Simulation, 20th International Shock Interaction Symposium, 20120820/0824, Stockholm (SE), pp.14, 2012 Abstract: In our earlier paper [3] we reported the investigation of the shock structure in dense, monatomic gas  argon. Here we extend our work to dense molecular gases and to liquids. We investigate, in particular, the influence of the electric charges (electric dipoles, quadrupoles etc.) of the molecules on the shock wave structure. Keywords:Shock structure, Dense media, Molecular Dynamics Affiliations:
 
6.  Słowicka A.M., Walenta Z.A., Szymański Z., Structure of the plume emitted during laser ablation of materials, ISSW28, 28th International Symposium on Shock Waves, 20110717/0722, Manchester (GB), pp.777782, 2012 Keywords: laser ablation, plume expansion, DSMC Affiliations:
 
7.  Walenta Z.A., Słowicka A.M., Structure of shock waves in dense media, ISSW28, 28th International Symposium on Shock Waves, 20110717/0722, Manchester (GB), pp.771776, 2012 Keywords: shock waves, dense fluids, molecular dynamics simulations Affiliations:

Conference abstracts
1.  Farutin A., Piasecki T., Słowicka A.M., Misbah C., Wajnryb E., EkielJeżewska M.L., Accumulation of vesicles and flexible fibers in unbounded Poiseuille flow, FLOWING MATTER 2017, 20170123/0127, Porto (PT), pp.37, 2017  
2.  Słowicka A.M., Stone H.A.^{♦}, EkielJeżewska M.L., Periodic motions of flexible fibers in shear flow, Bulletin of the American Physical Society, ISSN: 00030503, Vol.62, No.14, pp.221, 2017  
3.  EkielJeżewska M.L., Słowicka A.M., Wajnryb E., Dynamics of flexible fibers in shear flows, Flowing matter, 20160111/0115, Porto (PT), pp.7475, 2016  
4.  Słowicka A.M., Stone H.A.^{♦}, Wajnryb E., EkielJeżewska M.L., Three modes of the dynamics of flexible fibers in shear flow, ICTAM XXIV, 24th International Congress of Theoretical and Applied Mechanics, 20160821/0826, Montréal (CA), pp.11421143, 2016 Abstract: Dynamics of a single nonBrownian flexible fiber in shear flow at low Reynolds number is investigated numerically. Initially, the fiber is straight and at the equilibrium. For different initial orientations and values of bending stiffness, three generic scenarios are observed: the fiber tends to: align along the vorticity direction, tumble within the plane perpendicular to vorticity, or perform a periodic motion superposed with translation along the flow. Keywords:Stokes equations, flexible fibers, shear flow Affiliations:
 
5.  Farutin A.^{♦}, Piasecki T., Słowicka A.M., Misbah C.^{♦}, Wajnryb E., EkielJeżewska M.L., Migration of vesicles and flexible fibers in poiseuille flow, ICTAM XXIV, 24th International Congress of Theoretical and Applied Mechanics, 20160821/0826, Montréal (CA), pp.13441345, 2016 Abstract: Dynamics of flexible fibers and vesicles in unbounded planar Poiseuille flow at the lowReynoldsnumber are shown to exhibit similar basic features, when their equilibrium (moderate) aspect ratio is the same and vesicle viscosity contrast is relatively high. The lateral migration and accumulation of these two types of flexible objects are analyzed numerically. Keywords:Stokes equations, vesicles, flexible fibers Affiliations:
 
6.  Słowicka A.M., Wajnryb E., EkielJeżewska M.L., Flexible Fibers in Shear Flow, 6th International Symposium on Bifurcations and Instabilities in Fluid Dynamics, 20150715/0717, Paryż (FR), pp.61, 2015 Abstract: Modes of the dynamics of flexible fibers in shear flow in a plane perpendicular to vorticity are analyzed numerically. Stokes equations, flexible fibers, shear flow Affiliations:
 
7.  Słowicka A., Walenta Z., Szymański Z., Hoffman J., Mościcki T., Structure and expansion of a plume emitted during laser ablation of multicomponent materials, ISSW30, 30th International Symposium on Shock Waves, 20150719/0724, TelAviv (IL), pp.562571, 2015 Abstract: Pulsed laser deposition is a method frequently used for creating thin films of various materials on laser ablation, plume expansion, DSMC Affiliations:
 
8.  Walenta Z.A., Słowicka A.M., Similarity Parameters for Shock Waves in Dense Fluids, ISSW30, 30th International Symposium on Shock Waves, 20150719/0724, TelAviv (IL), pp.536537, 2015 Keywords: shock waves, dense fluids, molecular dynamics simulations Affiliations:
 
9.  Walenta Z.A., Słowicka A.M., Influence of moments of inertia of molecules on the structure of shocks in molecular liquids, KKNM, 4th National Conference on Nano and Micromechanics, 20140708/0710, Wrocław (PL), pp.76, 2014 Keywords: shock waves, dense media, molecular dynamics symulations Affiliations:
 
10.  Słowicka A.M., Wajnryb E., EkielJeżewska M.L., Migration of flexible fibers entrained by Poiseuille flow in microchannel, ICTAM XXIII, 23rd International Congress of Theoretical and Applied Mechanics, 20120819/0824, Beijing (CN), pp.12, 2012 Abstract: In this work, we consider a single nonBrownian mobile and flexible fiber immersed in Poiseuille flow in a channel consisting of two parallel infinite walls. The dynamics of the fiber is evaluated numerically from the Stokes equations by a multipole code HYDROMULTIPOLE. Investigating the fiber dynamics we found out that fibers migrate to a critical position across the channel. The distance between the wall and a limiting position depends on the fiber elongation and flexibility. For more stiff fibers the critical position results from the interplay between their tendency to drift away from the channel and the repulsive hydrodynamic interaction with the wall. For less stiff fibers the limiting position is not influenced by the presence of the wall. Differences between the critical position for different fibers can be used in the process of microfibers separation by the flow. Keywords:Stokes equations, hydrodynamic interactions, Poiseuille flow, flecible fiber Affiliations:
 
11.  Walenta Z.A., Słowicka A.M., Structure of shock waves in dense gases and liquids  Molecular Dynamics Simulation, III National Conference of Nano and Micromechanics, 20120704/0706, Warszawa (PL), pp.99100, 2012 Keywords: shock waves, dense fluids, molecular dynamics simulations Affiliations:
 
12.  Słowicka A.M., Wajnryb E., EkielJeżewska M.L., Migration of microfibers entrained by Poiseuille flow in microchannel, III National Conference of Nano and Micromechanics, 20120704/0706, Warszawa (PL), pp.7172, 2012 Keywords: Stokes equations, Poiseuille flow, flexible fibers, migration Affiliations:
