Simulation of Chain Organization in Encapsulated Polymers Peter Cifra, Tomas Bleha * Summary: The dimensional and structural properties of polymers confined into a cavity are computed by the Monte Carlo method as a function of the chain stiffness. The reduction of the size ratio <R 2 > / < R 2 g > close to 2, distinctive of compact spheres, is observed at squeezing of chains into a capsule. The plots of the static structure factor S(q) computed for stiff chains show characteristic humps attributed to the toroidal structure. The orientation correlation function is found to be a very sensitive indicator of the globule – toroid transition in encapsulated chains. Evidence is presented that the toroidal morphology is formed in stiff polymers when the capsule radius approaches the chain persistence length (D  P). Keywords: computer modeling; Monte Carlo simulation; nanoparticles; persistence length; polymer droplets; shape transition Introduction Encapsulation of polymer molecules into micro- and nano-spheres is fundamental to many technological and biological pro- cesses. [1,2] Polymer-filled capsules with the porous or hollow structure have found many applications, for example, in coating, printing and biomedical fields. Likewise, in microemulsion systems, the droplets con- fine the polymer chains inside a spherically closed space. Polymer droplets serve as microcarriers for a broad range of com- pounds in fluidic devices and drug delivery. Confinement of biopolymers into quasi- spherical spaces is also a ubiquitous phe- nomenon in nature. A prominent example is the double-stranded DNA packaged inside a bacteriophage capsid. Encapsula- tion of macromolecules by lipid membranes is used in study of protocellular structures under prebiotic conditions. As a rule, encapsulated polymers are confined into spaces that are much smaller than their natural size. For example, the dimension of a capsid, between 20 - 120 nm, is comparable to the persistence length of viral DNA (50 nm). Therefore, the encap- sulated macromolecules are forced to optimize their properties and chain orga- nization. Despite the considerable pro- gress, [3,4] the theoretical and experimental studies do not yet provide a complete picture of confinement effects in spherical cavities on the micro- and nanoscale. Unresolved issue of the internal organiza- tion of confined chains inside a cavity is of the considerable theoretical and practical interest. A notion of a disordered com- pressed coil (or a globule) is conventionally supposed for synthetic encapsulated poly- mers. In contrast, in DNA, the ‘‘condensa- tion’’ into the rather compact, ordered toroidal structure was established as a fundamental mechanism enabling the high density packing of DNA inside native confinements. [5] The aim of the present report is to explore by molecular simulations how the internal structure in a spherical capsule is affected by the chain stiffness. We have computed by the Monte Carlo method the dimensional and structural quantities of polymers of variable persistence length P confined into a sphere. Occurrence of the ‘‘shape transition’’ from the globular to Macromol. Symp. 2010, 296, 336–341 DOI: 10.1002/masy.201051046 336 Polymer Institute, Slovak Academy of Sciences, 842 36 Bratislava, Slovakia E-mail: bleha@savba.sk Copyright ß 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim wileyonlinelibrary.com