Soft nanoparticles (NPs) are emerging candidates for nano medicine, particularly for intercellular imaging and targeted drug delivery. Their soft nature, manifested in their dynamics, allows translocation into organisms without damaging their membranes. A crucial step towards incorporating soft dynamic NPs in nano medicine, is to resolve their interrelation with membranes. Here using atomistic molecular dynamics (MD) simulations we probe the interaction of soft NPs formed by conjugated polymers with a model membrane. These NPs, often termed polydots, are confined to their nano dimensions without any chemical tethers, forming dynamic long lived nano structures. Specifically, polydots formed by dialkylparapoly phenylene ethylene (PPE), with a varying number of carboxylate groups tethered to the alkyl chains to tune the interfacial charge of the surface of the NP are investigated at the interface with a model membrane that consists of di-palmitoyl phosphatidylcholine (DPPC). We find that even though polydots are controlled only by physical forces, they retain their NP configuration as they transcend the membrane. Regardless of their size, neutral polydots spontaneously penetrate the membrane whereas carboxylated polydots must be driven in, with a force that depends on the charge at their interface, all without significant disruption to the membrane. These fundamental results provide a means to control the position of the nanoparticles with respect to the membrane interfaces, which is key to their therapeutic use.