In this paper we study the following stochastic Hamiltonian system in ${\mathbb R}^{2d}$ (a second order stochastic differential equation), $$ d \dot X_t=b(X_t,\dot X_t)d t+\sigma(X_t,\dot X_t)d W_t,\ \ (X_0,\dot X_0)=(x,v)\in{\mathbb R}^{2d}, $$ where $b(x,v):{\mathbb R}^{2d}\to{\mathbb R}^d$ and $\sigma(x,v):{\mathbb R}^{2d}\to{\mathbb R}^d\otimes{\mathbb R}^d$ are two Borel measurable functions. We show that if $\sigma$ is bounded and uniformly non-degenerate, and $b\in H^{2/3,0}_p$ and $\nabla\sigma\in L^p$ for some $p>2(2d+1)$, where $H^{\alpha,\beta}_p$ is the Bessel potential space with differentiability indices $\alpha$ in $x$ and $\beta$ in $v$, then the above stochastic equation admits a unique strong solution so that $(x,v)\mapsto Z_t(x,v):=(X_t,\dot X_t)(x,v)$ forms a stochastic homeomorphism flow, and $(x,v)\mapsto Z_t(x,v)$ is weakly differentiable with ess.$\sup_{x,v}E\left(\sup_{t\in[0,T]}|\nabla Z_t(x,v)|^q\right)<\infty$ for all $q\geq 1$ and $T\geq 0$. Moreover, we also show the uniqueness of probability measure-valued solutions for kinetic Fokker-Planck equations with rough coefficients by showing the well-posedness of the associated martingale problem and using the superposition principle established by Figalli \cite{Fi} and Trevisan \cite{Tre}.
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